From owner-chemistry@ccl.net Mon Apr 18 02:00:00 2011 From: "Eliz Lam elizabeth.shlam_+_gmail.com" To: CCL Subject: CCL: Time consuming frequency calculations problem Message-Id: <-44399-110418015836-25165-PhtplYAgqcYB2ACRGxhR+w]_[server.ccl.net> X-Original-From: "Eliz Lam" Date: Mon, 18 Apr 2011 01:58:34 -0400 Sent to CCL by: "Eliz Lam" [elizabeth.shlam-$-gmail.com] Hi all, Thanks for all CCLers advice! However, after three days, I'm still stuck with the freq calculations. I've used freq=noraman with a 8 cores computer but it seems the calculations can't terminate even after three days. The functional I used is PBE1PBE with 6-31G** for C N H and sddall for metals. Since the maximum time allowed for me (a student) to work on the computer cluster is three days, I wonder when I restart the calculations, will the calculations start all over again or can it start from the position it terminates with some keywords? I'm wondering if there's an alternative to check whether my structure obtained is a minimum? Since I'm not interested in looking at the frequency at all but just simply want to check if my structure obtained is a minimum point. Thanks again! Regards, Eliz From owner-chemistry@ccl.net Mon Apr 18 03:38:01 2011 From: "Rudolf Herrmann rudolf.herrmann.:.physik.uni-augsburg.de" To: CCL Subject: CCL: problem in geometry optimization in GAMESS Message-Id: <-44400-110415120341-7299-m25xmzzjp/r3XxiLMoEmjg::server.ccl.net> X-Original-From: "Rudolf Herrmann" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 15 Apr 2011 18:03:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Rudolf Herrmann" [rudolf.herrmann ~~ physik.uni-augsburg.de] Dear Indu Kaul, > > Sent to CCL by: "indu kaul" [indu.kaul[a]iiserpune.ac.in] > I have recently started using GAMESS and facing the problem in geometry > optimization.Although it shows normal termination but certain bonds get > partiallized or broken.I have started for 7azaindole-2fluoropyridine dimer > and input file is given below: Your input file runs reasonably well on my Gamess(US) (version from January 2009), without any bond breaking or other anomalies. Of course NSTEP=20 is not enough to reach the equilibrium, but the tendency towards convergence is evident. With NSTEP=100 you should be fine. Cheers Rudolf. > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. $END > $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE DFTTYP=B3LYP $END > $STATPT OPTTOL=0.0001 NSTEP=20 $END > $SYSTEM TIMLIM=525600 MWORDS=45 MEMDDI=500 $END > $SCF DIRSCF=.True. $END > $DATA > title > C1 > C 6.0 1.84347900 0.04423200 -0.00007000 > C 6.0 3.15149200 0.61507500 0.00005800 > C 6.0 4.22613100 -0.27921800 0.00010900 > C 6.0 3.93635700 -1.63908700 0.00001600 > C 6.0 2.60050900 -2.07353000 -0.00010200 > C 6.0 1.62539300 2.26777600 0.00001600 > C 6.0 2.97807700 2.03763600 0.00006900 > H 1.0 5.25251900 0.07203200 0.00018900 > H 1.0 4.73149900 -2.37498000 0.00003700 > H 1.0 2.37878200 - 3.13677600 -0.00015600 > H 1.0 -0.07775500 0.95198800 -0.00010100 > H 1.0 1.08839400 3.20353400 0.00002200 > H 1.0 3.74900100 2.79215600 0.00012900 > N 7.0 0.93666300 1.07373300 -0.00006000 > C 6.0 -1.91328800 -1.15009000 -0.00007500 > C 6.0 -3.06849700 -1.92163300 0.00000100 > C 6.0 -4.30535900 -1.27448900 0.00009100 > C 6.0 -4.34833600 0.11436000 0.00010200 > C 6.0 -3.12382300 0.77131100 0.00001600 > N 7.0 -1.94635200 0.19570700 -0.00006700 > H 1.0 -5.22728200 -1.84452000 0.00015300 > H 1.0 -0.91970100 -1.59057200 -0.00014000 > H 1.0 -2.99985400 -3.00192900 -0.00000900 > H 1.0 -5.27388900 0.67407800 0.00016900 > N 7.0 1.54508400 -1.25461400 -0.00014500 > F 9.0 -3.11803300 2.11968300 0.00002500 > $END > Please help me to stop this bond breaking and partialization of bonds with > your suggestions. > > With Regards > Indu Kaul> -- Dr. Rudolf Herrmann Institut für Physik Universität Augsburg Universitätsstr. 1 D-86159 Augsburg Germany From owner-chemistry@ccl.net Mon Apr 18 04:13:00 2011 From: "Vivek Sharma vivek.viv.sharma[A]gmail.com" To: CCL Subject: CCL: HF method Message-Id: <-44401-110418014859-23777-euO59A0ppv2cIkqTxLAqGQ=server.ccl.net> X-Original-From: Vivek Sharma Content-Type: multipart/alternative; boundary=bcaec548a7f11c956a04a12af23c Date: Mon, 18 Apr 2011 08:48:49 +0300 MIME-Version: 1.0 Sent to CCL by: Vivek Sharma [vivek.viv.sharma,+,gmail.com] --bcaec548a7f11c956a04a12af23c Content-Type: text/plain; charset=ISO-8859-1 Hello, Please have a look to the pages 221-224 in the book, 'Molecular Quantum Mechanics, 4th Edition by Atkins and Friedman'. Exactly this point has been explained in detail. Briefly to mention, the exchange term is purely quantum mechanical phenomena, with no classical counterpart (like coulombic term has). The wavefunction when constructed in the sense of Slater Determinant, it leads to a positive exchange term, which is when subtracted from coulombic term, reduces the energy. Although, HF method deals with electron-electron interaction only in average way, so this reduction in energy may not be huge. I hope it helps. Vivek On 17 April 2011 13:47, bonoit bonoit bonoit_10!A!yahoo.fr < owner-chemistry/a\ccl.net> wrote: > > Sent to CCL by: "bonoit bonoit" [bonoit_10__yahoo.fr] > Dear CCLers, > I'm writing to enquire about the exchange term (Kij) in the Hartree-Fock > method. My question is as follow: > How c'd the exchange term reduce the energy in HF method? > And what c'd be the difference between this term and the coulombian one in > the same method HF? > Thank you in advance > Sincerely, > Bonoit> > > -- http://www.facebook.com/vivek.viv.sharma +358 50 5759 509 --bcaec548a7f11c956a04a12af23c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

Please have a look to the pages 221-224 in the book, 'Mol= ecular Quantum Mechanics, 4th Edition by Atkins and Friedman'. Exactly = this point has been explained in detail.

Briefly to mention, the exc= hange term is purely quantum mechanical phenomena, with no classical counte= rpart (like coulombic term has). The wavefunction when constructed in the s= ense of Slater Determinant, it leads to a positive exchange term, which is = when subtracted from coulombic term, reduces the energy. Although, HF metho= d deals with electron-electron interaction only in average way, so this red= uction in energy may not be huge.

I hope it helps.

Vivek

On 17 A= pril 2011 13:47, bonoit bonoit bonoit_10!A!yaho= o.fr <o= wner-chemistry/a\ccl.net> wrote:

Sent to CCL by: "bonoit =A0bonoit" [bonoit_10__yahoo.fr]
Dear CCLers,
I'm writing to enquire about the exchange term (Kij) in the Hartree-Foc= k method. My question is as follow:
How c'd the exchange term reduce the energy in HF method?
And what c'd be the difference between this term and the coulombian one= in the same method HF?
Thank you in advance
Sincerely,
Bonoit



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--bcaec548a7f11c956a04a12af23c-- From owner-chemistry@ccl.net Mon Apr 18 08:19:01 2011 From: "Gkourmpis, Thomas Thomas.Gkourmpis_._borealisgroup.com" To: CCL Subject: CCL:G: Time consuming frequency calculations problem Message-Id: <-44402-110418025851-8523-YCv88VTjz2c3y7n2pwhYDA*_*server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 18 Apr 2011 08:58:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis!=!borealisgroup.com] Eliz Hi Unfortunately in Gaussian the frequency calculations cannot be restarted by the keyword RESTART, so if the computation is stopped for any reason it must be restarted from the beginning, thus losing all the current results. Therefore stopping the computation after three days and restarting it is of no use. Since you're so limited in time why don't you check if your structure is at a minimum using a smaller basis set and a lower level of theory? It will not be as accurate, but at least you will have an indication before proceeding with much more expensive methods, Hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com*|*ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com*|*ccl.net] On Behalf Of Eliz Lam elizabeth.shlam_+_gmail.com Sent: Monday, April 18, 2011 7:59 AM To: Gkourmpis, Thomas Subject: CCL: Time consuming frequency calculations problem Sent to CCL by: "Eliz Lam" [elizabeth.shlam-$-gmail.com] Hi all, Thanks for all CCLers advice! However, after three days, I'm still stuck with the freq calculations. I've used freq=noraman with a 8 cores computer but it seems the calculations can't terminate even after three days. The functional I used is PBE1PBE with 6-31G** for C N H and sddall for metals. Since the maximum time allowed for me (a student) to work on the computer cluster is three days, I wonder when I restart the calculations, will the calculations start all over again or can it start from the position it terminates with some keywords? I'm wondering if there's an alternative to check whether my structure obtained is a minimum? Since I'm not interested in looking at the frequency at all but just simply want to check if my structure obtained is a minimum point. Thanks again! Regards, Elizhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Mon Apr 18 08:54:01 2011 From: "Eliz Lam elizabeth.shlam-#-gmail.com" To: CCL Subject: CCL:G: Time consuming frequency calculations problem Message-Id: <-44403-110418013915-26746-qcxJvpiPKK+T3Fu2BFThsw*o*server.ccl.net> X-Original-From: "Eliz Lam" Date: Mon, 18 Apr 2011 01:39:13 -0400 Sent to CCL by: "Eliz Lam" [elizabeth.shlam^gmail.com] Hi all, Thanks for all CCLers advice! However, after three days, I'm still stuck with the freq calculations. I've used freq=noraman with a 8 cores computer but it seems the calculations can't terminate even after three days. The functional I used is PBE1PBE with 6-31G** for C N H and sddall for metals. Since the maximum time allowed for me ( a student) to work on the computer cluster is three days, I wonder if I restart the calculations, will the calculations start all over again or can it start from the position it terminates with the keyword geom=check? I'm wondering if there's an alternative to check whether my structure obtained is a minimum? Since I'm not interested in looking at the frequency at all but just simply want to check if my structure obtained is a minimum point. Thanks again! Regards, Eliz > "Gkourmpis, Thomas Thomas.Gkourmpis^^^borealisgroup.com" wrote: > > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com] > Eliz Hi > > Generally speaking frequency calculations can be very time consuming depending on the number of molecules in the system, the potential energy surface around the minima and of course the level of theory and basis set you are using. Your system is quite big and if you're using MP-type methods with expanded basis sets waiting for a few days is perfectly natural (especially in less powerful computers). Once I had to wait for a week! > > As a rule of thumb as long as the program is working and doesn't produce any error or serious warning messages leave it alone. > > I hope this is helpful > > Thomas > > -----Original Message----- > > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com(!)ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com(!)ccl.net] On Behalf Of Eliz Lam elizabeth.shlam~!~gmail.com > Sent: Thursday, April 14, 2011 7:19 AM > To: Gkourmpis, Thomas > Subject: CCL:G: Time consuming frequency calculations problem > > > Sent to CCL by: "Eliz Lam" [elizabeth.shlam%a%gmail.com] > Hi all, > > I've been trying with the frequency calculations with gaussian03 for a molecule with 207 atoms to verify whether the geometry obtained from optimisation is a minimum. However, it seems that the frequency calculations have not been completed even after three days. I wonder is there something wrong, since I haven't done a frequency calculations which requires so much time? > > Thanks! > Elizhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and > intended solely for the use of the individual or the entity to whom > it is addressed. If you have received this Email by error, please > notify the sender and delete the material from any storage device. > Borealis extends no warranties and makes no representations as to > the accuracy or completeness of the information provided. It is the > customer's responsibility to inspect and test our products and > technical advice in order to satisfy itself as to the suitability > of the products and technical advice for the customer's particular > purpose. > > From owner-chemistry@ccl.net Mon Apr 18 09:47:00 2011 From: "Noel O Boyle baoilleach],[gmail.com" To: CCL Subject: CCL: Last chance to apply to attend Open Babel users' workshop Message-Id: <-44404-110418094229-22829-q2PtODUJTBc3kFqxRzvG2Q a server.ccl.net> X-Original-From: "Noel O Boyle" Date: Mon, 18 Apr 2011 09:42:26 -0400 Sent to CCL by: "Noel O Boyle" [baoilleach]-[gmail.com] Apply before April 22nd to attend the 2nd Open Babble (http://openbabel.org/wiki/2nd_Open_Babble), a hands-on Open Babel workshop presented by Open Babel developers Chris Morley, Tim Vandermeersch and Noel O'Boyle. This will take place on July 5-6 2011 at the Unilever Centre in the Dept of Chemistry, University of Cambridge, UK. This is the first ever users' workshop for Open Babel, one of the most widely used cheminformatics toolkits. Open Babble presents a unique opportunity to learn how to make the most of Open Babel, whether you are interested in using for converting file formats, writing scripts to analyse molecular structures, or developing your own chemistry software. The workshop will start on the afternoon of the 5th July, and finish on the evening of the 6th. The exact topics covered will depend on the attendees interests but will include some or all of the following: * Exploiting the Open Babel command line for fast searching and filtering of molecular databases * How to get the most from the Open Babel GUI * Getting started with Python scripting for chemistry * Compiling C++ programs that use Open Babel * Writing a new plugin for Open Babel * How to create a user-defined molecular fingerprint * Combining Open Babel with other Open Source cheminformatics toolkits To apply, visit the workshop website at: http://openbabel.org/wiki/2nd_Open_Babble Regards, Noel O'Boyle (on behalf of Open Babble organisers) From owner-chemistry@ccl.net Mon Apr 18 13:21:00 2011 From: "Raphael Martinez raphaelmartinez1983,,gmail.com" To: CCL Subject: CCL: Reaction Ratio Message-Id: <-44405-110418131536-27125-X61A8tlvbr9Xbd/v8YHH/Q],[server.ccl.net> X-Original-From: "Raphael Martinez" Date: Mon, 18 Apr 2011 13:15:34 -0400 Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983_-_gmail.com] Hi every one. I need a quick help. The starting material can give two products depending on the transition state. I have calculate the two transition states and I have the activation energy for both of them. The question is, how do I calculate the ratio between the two products using these activation energies?. This must be a simple equation, but I totally forgot how to this, and I am not able to find the answer searching in the internet. Thanks for the help. From owner-chemistry@ccl.net Mon Apr 18 14:50:01 2011 From: "Arne Dieckmann adieckma##googlemail.com" To: CCL Subject: CCL: Reaction Ratio Message-Id: <-44406-110418144359-28222-c0o4bspbQILXG1NVgrx67g^^^server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 18 Apr 2011 20:43:48 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Arne Dieckmann [adieckma*googlemail.com] Hi Raphael, try a quick search for "transition state theory" or "Eyring equation". This will allow you to calculate the rate constants and subsequently the rate of each reaction. Cheers, Arne On Apr 18, 2011, at 7:15 PM, Raphael Martinez raphaelmartinez1983,,gmail.com wrote: > > Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983_-_gmail.com] > Hi every one. I need a quick help. > The starting material can give two products depending on the transition state. I have calculate the two transition states and I have the activation energy for both of them. The question is, how do I calculate the ratio between the two products using these activation energies?. This must be a simple equation, but I totally forgot how to this, and I am not able to find the answer searching in the internet. > Thanks for the help.> > From owner-chemistry@ccl.net Mon Apr 18 15:24:00 2011 From: "Laleh Rezaei lalerezaei ~ gmail.com" To: CCL Subject: CCL:G: Converting 3D to 2D Message-Id: <-44407-110418142952-20929-h2pJNHhM45N0B78AA3Oj6g=-=server.ccl.net> X-Original-From: "Laleh Rezaei" Date: Mon, 18 Apr 2011 14:29:50 -0400 Sent to CCL by: "Laleh Rezaei" [lalerezaei]-[gmail.com] To whom it may concern, I am a graduate student in organic chemistry. As part of my project I need to work with Gaussian software. I faced a problem in converting 3D gaussian output to 2D. I am wondering if there any way that I can do it. I would be grateful if you could help me. Regards, Laleh From owner-chemistry@ccl.net Mon Apr 18 15:59:00 2011 From: "Sebastian Kozuch kozuchs*yahoo.com" To: CCL Subject: CCL: Reaction Ratio Message-Id: <-44408-110418145655-19139-JSIENBhnwSwxnF88kg2VOQ,server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-191514285-1303153006=:38996" Date: Mon, 18 Apr 2011 11:56:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs(~)yahoo.com] --0-191514285-1303153006=:38996 Content-Type: text/plain; charset=us-ascii In most cases (and according to the Courtin-Hammet principle) the Gibbs energy difference between the transition states gives the selectivity ratio. This will be for two products A and B: S=[A]/[B]=exp{[G(TS A)-G(TS B)]/RT} xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ....Weizmann Institute of Science.... ...........Rehovot, Israel........... .. sebastian.kozuch . weizmann.ac.il .. http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ________________________________ > From: "Raphael Martinez raphaelmartinez1983,,gmail.com" To: "Kozuch, Sebastian " Sent: Mon, April 18, 2011 2:15:34 PM Subject: CCL: Reaction Ratio Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983_-_gmail.com] Hi every one. I need a quick help. The starting material can give two products depending on the transition state. I have calculate the two transition states and I have the activation energy for both of them. The question is, how do I calculate the ratio between the two products using these activation energies?. This must be a simple equation, but I totally forgot how to this, and I am not able to find the answer searching in the internet. Thanks for the help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-191514285-1303153006=:38996 Content-Type: text/html; charset=us-ascii
In most cases (and according to the Courtin-Hammet principle) the Gibbs energy difference between the transition states gives the selectivity ratio. This will be for two products A and B: S=[A]/[B]=exp{[G(TS A)-G(TS B)]/RT}
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...........
.. sebastian.kozuch . weizmann.ac.il ..
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


From: "Raphael Martinez raphaelmartinez1983,,gmail.com" <owner-chemistry . ccl.net>
To: "Kozuch, Sebastian " <kozuchs . yahoo.com>
Sent: Mon, April 18, 2011 2:15:34 PM
Subject: CCL: Reaction Ratio


Sent to CCL by: "Raphael  Martinez" [raphaelmartinez1983_-_gmail.com]
Hi every one. I need a quick help.
The starting material can give two products depending on the transition state. I have calculate the two transition states and I have the activation energy for both of them. The question is, how do I calculate the ratio between the two products using these activation energies?. This must be a simple equation, but I totally forgot how to this, and I am not able to find the answer searching in the internet.
Thanks for the help.



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--0-191514285-1303153006=:38996-- From owner-chemistry@ccl.net Mon Apr 18 16:41:01 2011 From: "Mikael Johansson mikael.johansson!A!iki.fi" To: CCL Subject: CCL: Time consuming frequency calculations problem Message-Id: <-44409-110418163705-16741-MSquwZAphOneGZ3KEO+lqA:server.ccl.net> X-Original-From: Mikael Johansson Content-ID: Content-Type: MULTIPART/MIXED; BOUNDARY="-696237619-1282356729-1303158790=:28607" Date: Mon, 18 Apr 2011 23:36:53 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson ~ iki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696237619-1282356729-1303158790=:28607 Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-15; FORMAT=flowed Content-Transfer-Encoding: 8BIT Content-ID: Hola! On Mon, 18 Apr 2011, Eliz Lam elizabeth.shlam-#-gmail.com wrote: > I'm wondering if there's an alternative to check whether my structure > obtained is a minimum? Since I'm not interested in looking at the > frequency at all but just simply want to check if my structure obtained > is a minimum point. Don´t know if it is implemented in the code you are using, but algorithms have been devised in order to compute only a selected number of the lowest frequencies, usually at significantly reduced cost compared to getting the complete spectrum; in your case, computing just one freq would suffice. I´m outside anything more fancy than terminal access to the net, so cannot provide a proper reference (Furche at al, I´m almost sure, though), but have a look at the Turbomole manual and the description of the $les keyword. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ ---696237619-1282356729-1303158790=:28607-- From owner-chemistry@ccl.net Mon Apr 18 17:15:00 2011 From: "Wolf-D. Ihlenfeldt wdi/a\xemistry.com" To: CCL Subject: CCL:G: AW: G: Converting 3D to 2D Message-Id: <-44410-110418161327-27749-kzgbH9MUCpv1LUJ44RrEUg]![server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 18 Apr 2011 22:13:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi|,|xemistry.com] Do you mean generation of 2D schematic structure drawings from Gaussian Output files? You can do that with the Cactvs toolkit (www.xemistry.com/academic, free for academic users). Gaussian output is not exactly a precisely defined format, though - if the current release does not work for you, please send me a sample output. > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+wdi==xemistry.com]^[ccl.net [mailto:owner- > chemistry+wdi==xemistry.com]^[ccl.net] Im Auftrag von Laleh Rezaei > lalerezaei ~ gmail.com > Gesendet: Montag, 18. April 2011 20:30 > An: Ihlenfeldt, Wolf D > Betreff: CCL:G: Converting 3D to 2D > > > Sent to CCL by: "Laleh Rezaei" [lalerezaei]-[gmail.com] > > To whom it may concern, > > I am a graduate student in organic chemistry. As part of my project I > need to work with Gaussian software. I faced a problem in converting 3D > gaussian output to 2D. I am wondering if there any way that I can do > it. I would be grateful if you could help me. > > Regards, > Laleh> To recover the email address of the author of the message, please > change From owner-chemistry@ccl.net Mon Apr 18 17:50:00 2011 From: To: CCL Subject: CCL:G: End of file in GetChg Message-Id: <-44411-110418165932-4020-g2Rn+p48ILQb8jVRdekmoQ!A!server.ccl.net> X-Original-From: "" Content-Language: en-US Content-Type: multipart/alternative; boundary=_000_96C1CC302A4AF34393106B9F0978B91701B4F9EXMB02srnsandiago_ Date: Mon, 18 Apr 2011 20:59:09 +0000 MIME-Version: 1.0 Sent to CCL by: "" --_000_96C1CC302A4AF34393106B9F0978B91701B4F9EXMB02srnsandiago_ Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Hi, I have an input file that works, it does like 10 cycles and then the calcul= ation stops because of the following message I have tried to increase the memory but it doesn't do anything. Any help pl= ease ? thank you ...INPUT FILE.... %NProcShared=3D8 %chk=3Dcheckpointfile.chk %mem=3D20gb #p B3LYP gen scf=3D(maxcycle=3D100) opt(maxcycle=3D100) opt Gfinput IOP(6/7= =3D3) Pop=3Dfull scrf=3Dpcm CH3_amide_Trans_I3-_bas_perpendiculaire (0K, 1 atmosphere, optimisation de = la molecule avec PCM) -1 1 I1 -4.061393967 -5.223549697 2.613409149 I2 -4.354799778 -4.727022534 0.016685394 I3 -4.488225627 -4.487532712 -2.629149564 C1 -8.002808433 -0.728256378 0.000000000 C2 -7.006281495 0.416620459 -0.000000000 N1 -5.700288675 0.053390885 -0.000000000 O1 -7.379639623 1.588603651 -0.000000000 C3 -4.603660253 1.008031785 -0.000000000 H1 -7.539284757 -1.715244581 0.001000000 H2 -8.641212087 -0.634977881 -0.880999982 H3 -8.642493737 -0.634380168 0.879999995 H4 -5.474790400 -0.928712228 -0.000000000 H5 -3.978063560 0.885615861 -0.888000011 H6 -3.979345210 0.886213575 0.888999999 H7 -5.031817774 2.008956460 -0.001000000 H C O N 0 6-311G** **** I 0 S 5 1.00 444750.0000000 0.0008900 66127.0000000 0.0069400 14815.0000000 0.0360900 4144.9000000 0.1356800 1361.2000000 0.3387800 S 2 1.00 508.4400000 0.4365900 209.5900000 0.1837500 S 1 1.00 81.9590000 1.0000000 S 1 1.00 36.8050000 1.0000000 S 1 1.00 13.4950000 1.0000000 S 1 1.00 6.8859000 1.0000000 S 1 1.00 2.5520000 1.0000000 S 1 1.00 1.2088000 1.0000000 S 1 1.00 0.2734000 1.0000000 S 1 1.00 0.1009000 1.0000000 P 4 1.00 2953.6000000 0.0122100 712.6100000 0.0858700 236.7100000 0.2949300 92.6310000 0.4784900 P 1 1.00 39.7320000 1.0000000 P 1 1.00 17.2730000 1.0000000 P 1 1.00 7.9570000 1.0000000 P 1 1.00 3.1529000 1.0000000 P 1 1.00 1.3328000 1.0000000 P 1 1.00 0.4947000 1.0000000 P 1 1.00 0.2160000 1.0000000 P 1 1.00 0.0829300 1.0000000 D 3 1.00 261.9500000 0.0314400 76.7340000 0.1902800 27.5510000 0.4724700 D 1 1.00 10.6060000 1.0000000 D 1 1.00 3.4217000 1.0000000 D 1 1.00 1.1370000 1.0000000 D 1 1.00 0.3020000 1.0000000 **** 80.0 300 .....RESULT WHEN THE CALCULATION IS STOPPED.... Total kinetic energy from orbitals=3D 2.100481510469D+04 No NMR shielding tensors so no spin-rotation constants. Leave Link 601 at Mon Apr 18 15:55:17 2011, MaxMem=3D 2684354560 cpu: = 7.7 (Enter /apps/gaussian/intel/g09/l107.exe) Allocation: ICR=3D 1 ICP=3D 46 IAnSav=3D 91 IRI=3D 106 IWt=3D 1141 IDP=3D 2176 ICScr=3D 2221 IRC=3D 2266 IC=3D 3301 IX=3D 4381 IDF=3D 4426 IDDF=3D 4471 IXInc=3D 6496 IEVal=3D 6541 IEVec=3D 6586 IScr1=3D 8611 IScr2=3D 8656 IEnd=3D 8700 Recover reactant geometry. Energy =3D -0.21007388D+05 Leave Link 107 at Mon Apr 18 15:55:17 2011, MaxMem=3D 2684354560 cpu: = 0.0 (Enter /apps/gaussian/intel/g09/l101.exe) -------- 80.0 300 -------- Symbolic Z-matrix: End of file in GetChg. Error termination via Lnk1e in /apps/gaussian/intel/g09/l101.exe at Mon Ap= r 18 15:55:17 2011. Job cpu time: 0 days 0 hours 11 minutes 34.1 seconds. File lengths (MBytes): RWF=3D 112 Int=3D 0 D2E=3D 0 Chk=3D = 7 Scr=3D 1 --_000_96C1CC302A4AF34393106B9F0978B91701B4F9EXMB02srnsandiago_ Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: quoted-printable
Hi,
 
I have an input file that works, it does like 10 cycles and then the c= alculation stops because of the following message
I have tried to increase the memory but it doesn't do anything. Any he= lp please ?
 
thank you
 
...INPUT FILE....
 
%NProcShared=3D8
%chk=3Dcheckpointfile.chk
%mem=3D20gb
#p B3LYP gen scf=3D(maxcycle=3D100) opt(maxcycle=3D100) opt Gfinput IO= P(6/7=3D3) Pop=3Dfull scrf=3Dpcm
 
CH3_amide_Trans_I3-_bas_perpendiculaire (0K, 1 atmosphere, optimisatio= n de la molecule avec PCM)
 
-1 1
I1      -4.061393967   -5.223549697=     2.613409149
I2      -4.354799778   -4.727022534=     0.016685394
I3      -4.488225627   -4.487532712=    -2.629149564
C1      -8.002808433   -0.728256378=     0.000000000
C2      -7.006281495    0.4166= 20459   -0.000000000
N1      -5.700288675    0.0533= 90885   -0.000000000
O1      -7.379639623    1.5886= 03651   -0.000000000
C3      -4.603660253    1.0080= 31785   -0.000000000
H1      -7.539284757   -1.715244581=     0.001000000
H2      -8.641212087   -0.634977881=    -0.880999982
H3      -8.642493737   -0.634380168=     0.879999995
H4      -5.474790400   -0.928712228=    -0.000000000
H5      -3.978063560    0.8856= 15861   -0.888000011
H6      -3.979345210    0.8862= 13575    0.888999999
H7      -5.031817774    2.0089= 56460   -0.001000000
 
H C O N 0
6-311G**      
****
I 0
S   5   1.00
444750.0000000         &= nbsp;    0.0008900       =
  66127.0000000        &n= bsp;     0.0069400      &= nbsp;
  14815.0000000        &n= bsp;     0.0360900      &= nbsp;
   4144.9000000       &nb= sp;      0.1356800     &n= bsp; 
   1361.2000000       &nb= sp;      0.3387800     &n= bsp; 
S   2   1.00
    508.4400000      &nbs= p;       0.4365900    &nb= sp;  
    209.5900000      &nbs= p;       0.1837500    &nb= sp;  
S   1   1.00
     81.9590000      = ;        1.0000000   &nbs= p;   
S   1   1.00
     36.8050000      = ;        1.0000000   &nbs= p;   
S   1   1.00
     13.4950000      = ;        1.0000000   &nbs= p;   
S   1   1.00
      6.8859000     =          1.0000000   = ;    
S   1   1.00
      2.5520000     =          1.0000000   = ;    
S   1   1.00
      1.2088000     =          1.0000000   = ;    
S   1   1.00
      0.2734000     =          1.0000000   = ;    
S   1   1.00
      0.1009000     =          1.0000000   = ;    
P   4   1.00
   2953.6000000       &nb= sp;      0.0122100     &n= bsp; 
    712.6100000      &nbs= p;       0.0858700    &nb= sp;  
    236.7100000      &nbs= p;       0.2949300    &nb= sp;  
     92.6310000      = ;        0.4784900   &nbs= p;   
P   1   1.00
     39.7320000      = ;        1.0000000   &nbs= p;   
P   1   1.00
     17.2730000      = ;        1.0000000   &nbs= p;   
P   1   1.00
      7.9570000     =          1.0000000   = ;    
P   1   1.00
      3.1529000     =          1.0000000   = ;    
P   1   1.00
      1.3328000     =          1.0000000   = ;    
P   1   1.00
      0.4947000     =          1.0000000   = ;    
P   1   1.00
      0.2160000     =          1.0000000   = ;    
P   1   1.00
      0.0829300     =          1.0000000   = ;    
D   3   1.00
    261.9500000      &nbs= p;       0.0314400    &nb= sp;  
     76.7340000      = ;        0.1902800   &nbs= p;   
     27.5510000      = ;        0.4724700   &nbs= p;   
D   1   1.00
     10.6060000      = ;        1.0000000   &nbs= p;   
D   1   1.00
      3.4217000     =          1.0000000   = ;    
D   1   1.00
      1.1370000     =          1.0000000   = ;    
D   1   1.00
      0.3020000     =          1.0000000
****
 
80.0 300
 
.....RESULT WHEN THE CALCULATION IS STOPPED....
 
Total kinetic energy from orbitals=3D 2.100481510469D+04
No NMR shielding tensors so no spin-rotation constants.
Leave Link  601 at Mon Apr 18 15:55:17 2011, MaxMem=3D 268435456= 0 cpu:       7.7
(Enter /apps/gaussian/intel/g09/l107.exe)
Allocation:
     ICR=3D      1 &= nbsp;  ICP=3D     46 IAnSav=3D   &n= bsp; 91
     IRI=3D    106   = ; IWt=3D   1141    IDP=3D   2176  I= CScr=3D   2221
     IRC=3D   2266   &nbs= p; IC=3D   3301     IX=3D   4381&nb= sp;   IDF=3D   4426
    IDDF=3D   4471  IXInc=3D  = 6496  IEVal=3D   6541  IEVec=3D   6586
   IScr1=3D   8611  IScr2=3D   8656=    IEnd=3D   8700
Recover reactant geometry.  Energy =3D -0.21007388D+05
Leave Link  107 at Mon Apr 18 15:55:17 2011, MaxMem=3D 268435456= 0 cpu:       0.0
(Enter /apps/gaussian/intel/g09/l101.exe)
--------
80.0 300
--------
Symbolic Z-matrix:
End of file in GetChg.
Error termination via Lnk1e in /apps/gaussian/intel/g09/l101.exe at M= on Apr 18 15:55:17 2011.
Job cpu time:  0 days  0 hours 11 minutes 34.1 seconds.
File lengths (MBytes):  RWF=3D    112 Int=3D = ;     0 D2E=3D      0 Chk=3D&n= bsp;     7 Scr=3D      1
 
&nbs= p;
&nbs= p;
 --_000_96C1CC302A4AF34393106B9F0978B91701B4F9EXMB02srnsandiago_-- From owner-chemistry@ccl.net Mon Apr 18 18:25:00 2011 From: "Cory Pye cpye---ap.smu.ca" To: CCL Subject: CCL:G: Time consuming frequency calculations problem Message-Id: <-44412-110418132106-3771-z2235HnJG1SbGN5xCH+Lrw**server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 18 Apr 2011 14:26:10 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye-#-ap.smu.ca] Hello Eliz, Submit the job using Freq=(Numer) then Freq=(Numer,Restart) each time you resubmit. Analytic Frequencies cannot be restarted but numerical frequencies can be, since it essentially just a finite difference approach over all the coordinates. This might take significantly longer than doing Freq by itself, but you will (eventually) get a set of frequencies. This is helpful if you don't have the computational resources (or quota) that you need for an analytical frequencies. -Cory On Mon, 18 Apr 2011, Eliz Lam elizabeth.shlam-#-gmail.com wrote: > > Sent to CCL by: "Eliz Lam" [elizabeth.shlam^gmail.com] > Hi all, > > Thanks for all CCLers advice! However, after three days, I'm still stuck with the freq calculations. I've used freq=noraman with a 8 cores computer but it seems the calculations can't terminate even after three days. The functional I used is PBE1PBE with 6-31G** for C N H and sddall for metals. > Since the maximum time allowed for me ( a student) to work on the computer cluster is three days, I wonder if I restart the calculations, will the calculations start all over again or can it start from the position it terminates with the keyword geom=check? > I'm wondering if there's an alternative to check whether my structure obtained is a minimum? Since I'm not interested in looking at the frequency at all but just simply want to check if my structure obtained is a minimum point. > > Thanks again! > Regards, > Eliz > > > > "Gkourmpis, Thomas Thomas.Gkourmpis^^^borealisgroup.com" wrote: > > > > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com] > > Eliz Hi > > > > Generally speaking frequency calculations can be very time consuming depending on the number of molecules in the system, the potential energy surface around the minima and of course the level of theory and basis set you are using. Your system is quite big and if you're using MP-type methods with expanded basis sets waiting for a few days is perfectly natural (especially in less powerful computers). Once I had to wait for a week! > > > > As a rule of thumb as long as the program is working and doesn't produce any error or serious warning messages leave it alone. > > > > I hope this is helpful > > > > Thomas > > > > -----Original Message----- > > > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com(!)ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com(!)ccl.net] On Behalf Of Eliz Lam elizabeth.shlam~!~gmail.com > > Sent: Thursday, April 14, 2011 7:19 AM > > To: Gkourmpis, Thomas > > Subject: CCL:G: Time consuming frequency calculations problem > > > > > > Sent to CCL by: "Eliz Lam" [elizabeth.shlam%a%gmail.com] > > Hi all, > > > > I've been trying with the frequency calculations with gaussian03 for a molecule with 207 atoms to verify whether the geometry obtained from optimisation is a minimum. However, it seems that the frequency calculations have not been completed even after three days. I wonder is there something wrong, since I haven't done a frequency calculations which requires so much time? > > > > Thanks! > > Elizhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and > > intended solely for the use of the individual or the entity to whom > > it is addressed. If you have received this Email by error, please > > notify the sender and delete the material from any storage device. > > Borealis extends no warranties and makes no representations as to > > the accuracy or completeness of the information provided. It is the > > customer's responsibility to inspect and test our products and > > technical advice in order to satisfy itself as to the suitability > > of the products and technical advice for the customer's particular > > purpose.> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye(-)crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Mon Apr 18 19:00:00 2011 From: "Miguel Quiliano Meza rifaximina:_:gmail.com" To: CCL Subject: CCL: LUDI program Message-Id: <-44413-110418180941-19568-bMuqtliNwZzzw8VgtMiP9A^server.ccl.net> X-Original-From: Miguel Quiliano Meza Content-Type: multipart/alternative; boundary=001636920a1a6f018f04a138a576 Date: Mon, 18 Apr 2011 18:09:32 -0400 MIME-Version: 1.0 Sent to CCL by: Miguel Quiliano Meza [rifaximina#gmail.com] --001636920a1a6f018f04a138a576 Content-Type: text/plain; charset=ISO-8859-1 Dear community. I would like to know if there are users of LUDI at forum. Thanks in advance. Miguel Quiliano --001636920a1a6f018f04a138a576 Content-Type: text/html; charset=ISO-8859-1 Dear community.

I would like to know if there are users of LUDI at forum.

Thanks in advance.

Miguel Quiliano



--001636920a1a6f018f04a138a576-- From owner-chemistry@ccl.net Mon Apr 18 19:46:00 2011 From: "Vlad vvv900,+,anusf.anu.edu.au" To: CCL Subject: CCL:G: Converting 3D to 2D Message-Id: <-44414-110418193909-2823-UZ1Z/jtBPM1r/gwErsUHWQ[]server.ccl.net> X-Original-From: Vlad Content-transfer-encoding: 7BIT Content-type: text/html; CHARSET=US-ASCII Date: Tue, 19 Apr 2011 09:38:12 +1000 MIME-version: 1.0 Sent to CCL by: Vlad [vvv900],[anusf.anu.edu.au] Hi Laleh,

> I am a graduate student in organic chemistry. As part of my project I
> need to work with Gaussian software. I faced a problem in converting
> 3D gaussian output to 2D. I am wondering if there any way that I can
> do it. I would be grateful if you could help me.

I suggest you to try Jamberoo.

Jamberoo can parse both the input and output Gaussian files. In the case of the output files Jamberoo can extract the optimization information and frequencies data and plot them using the interactive charting. It can also animate vibrations. Jamberoo can also parse Gaussian cube files and visualize the volumetric data (MOs, electrostatic potential).

As for the data presentation you have several options in Jamberoo:

1) You can create the jpeg or png image of your molecular scene.

2) For the high quality graphics you can create input file for the PovRay.

3) Finally, you can create a file in the VRML format and use it for creation of the 3D PDF documents.

Regards,
Vlad
From owner-chemistry@ccl.net Mon Apr 18 20:39:00 2011 From: "upendra adhikari upendra.adhikari%x%aggiemail.usu.edu" To: CCL Subject: CCL: Transition state calculation Message-Id: <-44415-110418190737-7061-WmEaavXOd17XOV31rUtqMw]=[server.ccl.net> X-Original-From: "upendra adhikari" Date: Mon, 18 Apr 2011 19:07:33 -0400 Sent to CCL by: "upendra adhikari" [upendra.adhikari:aggiemail.usu.edu] Hello all! I am doing some calculations on transition state, I got some negative frequencies ranging from -100 to -600, Is their any relation of this with geometry or barrier height or anything else?. I will appreciate if you can post some papers related to that. Thank You Upendra From owner-chemistry@ccl.net Mon Apr 18 21:14:00 2011 From: "upendra adhikari upendra.adhikari-$-aggiemail.usu.edu" To: CCL Subject: CCL: Transition state calculation Message-Id: <-44416-110418191154-11683-aaDUj9UZEfjEkzLElTdzkQ_._server.ccl.net> X-Original-From: "upendra adhikari" Date: Mon, 18 Apr 2011 19:11:52 -0400 Sent to CCL by: "upendra adhikari" [upendra.adhikari^^aggiemail.usu.edu] Hello all! I am doing some calculations on transition state, I got some negative frequencies ranging from -100 to -600, Is their any relation of this with geometry or barrier height or anything else? Thank You Upendra