From owner-chemistry@ccl.net Fri Nov 10 05:56:01 2006 From: "Caroline Norris cn29-.-sussex.ac.uk" To: CCL Subject: CCL: Ab initio excited states Message-Id: <-32991-061110053915-24270-HqETSI38acGMNhMgTbi98A _ server.ccl.net> X-Original-From: "Caroline Norris" Date: Fri, 10 Nov 2006 05:39:11 -0500 Sent to CCL by: "Caroline Norris" [cn29#sussex.ac.uk] Thanks again to all who replied to my last e-mail. I do have one more question though. What is the best way to calculate excited states using couple cluster or configuration interaction methods (I already use CIS)? I want to perform excited state scans, and is there any way in which I can be sure that I am sitting on the correct wavefunction? Thanks in advance, Caroline Norris cn29 .. sussex.ac.uk From owner-chemistry@ccl.net Fri Nov 10 07:49:00 2006 From: "Gisele Freitas Gauze giselegauze%a%yahoo.com.br" To: CCL Subject: CCL: who determine this interaction? Message-Id: <-32992-061110073904-30835-Po7VVrXiOm/fIOnJYe5r7w%x%server.ccl.net> X-Original-From: "Gisele Freitas Gauze" Date: Fri, 10 Nov 2006 07:39:03 -0500 Sent to CCL by: "Gisele Freitas Gauze" [giselegauze{}yahoo.com.br] I would like to known if is possible to calculated/determine the interaction between two compounds, that have the R-SO3....C=O groups. Can I consider this type of interactions as a transitional state? Thanks in advance, Gisele de Freitas Gauze giselegauze|yahoo.com.br From owner-chemistry@ccl.net Fri Nov 10 08:45:00 2006 From: "Oscar Julian Astudillo osastudi . icaro.dic.uchile.cl" To: CCL Subject: CCL:G: Molybdenum Calculations in G03W Message-Id: <-32993-061110003927-21446-HeFiZBrGFuaGkE6tH9qaZw[#]server.ccl.net> X-Original-From: "Oscar Julian Astudillo" Date: Fri, 10 Nov 2006 00:39:27 -0500 Sent to CCL by: "Oscar Julian Astudillo" [osastudi..icaro.dic.uchile.cl] Dear members. I'm trying to run a calculation in gaussian 03, but i want to use different basis sets for the components. I want to use the Lanl2DZ basis set for the molybdenum atoms and 6-31G** for the others (C, H, O, and F). I don't know hoy to do that. I read the help, but i can't start the job. This is the error message: WANTED AN INTEGER AS INPUT. FOUND A STRING AS INPUT. C H O F 0 This is the input file: =============================================================================== %chk=F:/Mo4TFa8Dioxane/Mo4TFa8/Lanl2DZ(DF).chk %mem=1225Mb %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=10000MB ----------------------------------------- p b3lyp/Gen guess=save geom=connectivity ----------------------------------------- 1/38=1,57=2/1; 2/17=6,18=5,40=1/2; 3/5=7,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4//1; 5/5=2,32=1,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Fri Nov 10 02:24:52 2006, MaxMem= 160563200 cpu: 2.0 (Enter c:\archivos de programa\G03\l101.exe) ----------------------------------- Mo2TFa4--Mo2Tfa4 DFT/Lanl2DZ+6-31** ----------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 molecule specification WANTED AN INTEGER AS INPUT. FOUND A STRING AS INPUT. C H O F 0 ============================================================================= Please, if any person could help me, i would be very thankful From owner-chemistry@ccl.net Fri Nov 10 09:19:01 2006 From: "Betty Coussens betty.coussens]=[dsm.com" To: CCL Subject: CCL: Dacapo Message-Id: <-32994-061110085046-4179-BXf4oXJGMLJqud5nvITAFA^_^server.ccl.net> X-Original-From: "Betty Coussens" Date: Fri, 10 Nov 2006 08:50:45 -0500 Sent to CCL by: "Betty Coussens" [betty.coussens * dsm.com] Dear all, We would like to study the interaction of reasonably sized organic molecules like di-n-butyl-phthalate with various surfaces of alpha and beta MgCl2. We therefore want to implement a periodic plane wave code on our PC cluster. Of course several commercial codes are available such as CPMD, CASTEP etc. However, all of these codes cost a lot of money. Looking on the internet and the available literature it seems that a freeware code like Dacapo might be a good choice as well. Can anybody comment on this? Thanks in advance! Betty From owner-chemistry@ccl.net Fri Nov 10 09:54:00 2006 From: "Filipe J. S. Duarte duarte ~~ staff.uni-marburg.de" To: CCL Subject: CCL:G: Molybdenum Calculations in G03W Message-Id: <-32995-061110094747-8606-hCtCYJtpARj6C3rljWVD0g : server.ccl.net> X-Original-From: "Filipe J. S. Duarte" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 10 Nov 2006 15:08:25 +0100 MIME-Version: 1.0 Sent to CCL by: "Filipe J. S. Duarte" [duarte-$-staff.uni-marburg.de] Hello Try to use this type of imput %Chk=(...) %mem=(...) # B3LYP/gen pseudo=read Opt (...) Maxdisk=15800Mb Title Charge = (...) Multiplicity = (...) molecule coordinates C H O F 0 6-31G** **** Mo 0 lanl2dz **** Mo 0 lanl2dz Good luck Oscar Julian Astudillo osastudi . icaro.dic.uchile.cl escreveu: > Sent to CCL by: "Oscar Julian Astudillo" [osastudi..icaro.dic.uchile.cl] > Dear members. > I'm trying to run a calculation in gaussian 03, but i want to use different basis sets for the components. I want to use the Lanl2DZ basis set for the molybdenum atoms and 6-31G** for the others (C, H, O, and F). I don't know hoy to do that. I read the help, but i can't start the job. > This is the error message: > > WANTED AN INTEGER AS INPUT. > FOUND A STRING AS INPUT. > C H O F 0 > > This is the input file: > =============================================================================== > %chk=F:/Mo4TFa8Dioxane/Mo4TFa8/Lanl2DZ(DF).chk > %mem=1225Mb > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=10000MB > ----------------------------------------- > p b3lyp/Gen guess=save geom=connectivity > ----------------------------------------- > 1/38=1,57=2/1; > 2/17=6,18=5,40=1/2; > 3/5=7,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4//1; > 5/5=2,32=1,38=5/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 99/5=1,9=1/99; > Leave Link 1 at Fri Nov 10 02:24:52 2006, MaxMem= 160563200 cpu: 2.0 > (Enter c:\archivos de programa\G03\l101.exe) > ----------------------------------- > Mo2TFa4--Mo2Tfa4 DFT/Lanl2DZ+6-31** > ----------------------------------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > > molecule specification > > WANTED AN INTEGER AS INPUT. > FOUND A STRING AS INPUT. > C H O F 0 > > ============================================================================= > Please, if any person could help me, i would be very thankful> > > > > -- Filipe J. S. Duarte Ph. D. Student Fachbereich Chemie AK FrenKing Philipps-Universität Marburg Hans-Meerwein-Strasse D-35032 Marburg Germany From owner-chemistry@ccl.net Fri Nov 10 10:29:01 2006 From: "Mark Jarvis Mark.Jarvis+/-colorado.edu" To: CCL Subject: CCL:G: Molybdenum Calculations in G03W Message-Id: <-32996-061110095426-9301-2MQoujLY+47KVWgYVJ67Yg^^server.ccl.net> X-Original-From: Mark Jarvis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 10 Nov 2006 07:54:16 -0700 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Mark Jarvis [Mark.Jarvis__colorado.edu] Hello, The first thing I noticed is that the charge and multiplicity should be in one line, after the title section, before the geometry specification, simply as 0 1 You have given the output file here, so I can only guess this is your problem. However, it seems likely since the error was "WANTED AN INTEGER...." Hope this helps, Mark On Nov 10, 2006, at 6:47 AM, Oscar Julian Astudillo osastudi . icaro.dic.uchile.cl wrote: > Sent to CCL by: "Oscar Julian > Astudillo" [osastudi..icaro.dic.uchile.cl] > Dear members. > I'm trying to run a calculation in gaussian 03, but i want to use > different basis sets for the components. I want to use the Lanl2DZ > basis set for the molybdenum atoms and 6-31G** for the others (C, > H, O, and F). I don't know hoy to do that. I read the help, but i > can't start the job. > This is the error message: > > WANTED AN INTEGER AS INPUT. > FOUND A STRING AS INPUT. > C H O F 0 > > This is the input file: > ====================================================================== > ========= > %chk=F:/Mo4TFa8Dioxane/Mo4TFa8/Lanl2DZ(DF).chk > %mem=1225Mb > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=10000MB > ----------------------------------------- > p b3lyp/Gen guess=save geom=connectivity > ----------------------------------------- > 1/38=1,57=2/1; > 2/17=6,18=5,40=1/2; > 3/5=7,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4//1; > 5/5=2,32=1,38=5/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 99/5=1,9=1/99; > Leave Link 1 at Fri Nov 10 02:24:52 2006, MaxMem= 160563200 cpu: 2.0 > (Enter c:\archivos de programa\G03\l101.exe) > ----------------------------------- > Mo2TFa4--Mo2Tfa4 DFT/Lanl2DZ+6-31** > ----------------------------------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > > molecule specification > > WANTED AN INTEGER AS INPUT. > FOUND A STRING AS INPUT. > C H O F 0 > > ====================================================================== > ======= > Please, if any person could help me, i would be very thankful > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Fri Nov 10 11:04:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira#%#ist.utl.pt" To: CCL Subject: CCL:G: Dacapo Message-Id: <-32997-061110103953-1664-2shA/bRsWCgR6UiiMBhDUg{}server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 10 Nov 2006 14:59:19 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira_-_ist.utl.pt] Betty Coussens betty.coussens]=[dsm.com wrote: > Sent to CCL by: "Betty Coussens" [betty.coussens * dsm.com] > Dear all, > > We would like to study the interaction of reasonably sized organic molecules like di-n-butyl-phthalate with various surfaces of alpha and beta MgCl2. We therefore want to implement a periodic plane wave code on our PC cluster. Of course several commercial codes are available such as CPMD, CASTEP etc. However, all of these codes cost a lot of money. CPMD is free and is also available for Windows XP. It does however suffer from an extraordinary lack of user support. CASTEP does cost a lot of money (€10,749.00 to be exact) unless you are lucky enough to be in a UK university. Plenty of other codes around such as Gaussian03 and VASP (commercial), Abinit and PWSCF (free). Regards, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student :: IST,Lisbon -- From owner-chemistry@ccl.net Fri Nov 10 11:51:00 2006 From: "William Shirley bill,emolecules.com" To: CCL Subject: CCL: Chemical Structure Portal on the Web. Message-Id: <-32998-061110102651-29157-8y1/taWEwLu+kXS5+pwLug\a/server.ccl.net> X-Original-From: "William Shirley" Date: Fri, 10 Nov 2006 10:26:50 -0500 Sent to CCL by: "William Shirley" [bill()emolecules.com] Find chemical structures on the web using the www.eMolecules.com web site. eMolecules continues to have the largest structure searchable compound database on the web. Close to a thousand users each day find the information that they need by searching our site: drawing structures; typing a CAS number or compound name (or fraction of a name, e.g. *amide*). We continually update from vendor catalogs, public domain databases, and continue to improve links from our site into source material. It is now easier than ever to find a plethora of property data and spectra on the web by starting at our site. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Did you know that in addition to JME, you could use Chem or Isis Draw with our site? Set a preference and you too can cut and paste in or out of either drawing package: http://www.emolecules.com/cgi-bin/prefs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Want a sortable table view of your search results? Want to download an SD file or an XL workbook of structures, try our expert interface: http://advanced.emolecules.com/cgi-bin/rene/signup_public.cgi?GuestAccount=1 or hit the Expert Search button from the www.eMolecules.com home page. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If you have a web site, you can link to us: Text queries, e.g. viagra: http://www.emolecules.com/cgi-bin/search?t=ss&q=viagra Catalog or common source view, e.g. Sigma Aldrich: http://www.emolecules.com/cgi-bin/search?t=ss&q=c&v=Sigma+Aldrich and structure queries (with smiles), e.g. a big ring: http://www.emolecules.com/cgi-bin/chemistry?t=ex&q=C1CCCCCCCCC1 Finally, you can also embed our search engine into your web site: http://www.emolecules.com/doc/emolecules_free2.htm?verified=1&Submit=Get+the+Free+eMolecules+Code (Terms of service are at: (http://www.emolecules.com/doc/emolecules_free.htm) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Best regards, -Bill From owner-chemistry@ccl.net Fri Nov 10 12:26:01 2006 From: "srinivas raju g raju.g.srinivas^gmail.com" To: CCL Subject: CCL: difference between molecular modelling and molecular simulation Message-Id: <-32999-061110090431-16796-1ReyKP1JgkHXeavq04YZ0w###server.ccl.net> X-Original-From: "srinivas raju g" Date: Fri, 10 Nov 2006 09:04:30 -0500 Sent to CCL by: "srinivas raju g" [raju.g.srinivas,gmail.com] hi, i have just finished my Masters in chemistry and wish to take up computational chem. for research. i need little clarification in this regard. can someone explain the difference ( if any) between "molecular modelling" and "molecular simulation" . as far as i know "molecular simulation" is generally associated with liquids and gases but "molecular modelling" is associated with proteins organic molecules etc. can anyone explain their differences ( in terms of what one does during research in these areas). how are these two different in terms of application to industry? For example, is molecular dynamics/simulation applicable to drug design? regards, srinivas raju.g From owner-chemistry@ccl.net Fri Nov 10 13:01:01 2006 From: "davidofkozlowski davidofkozlowski*gmail.com" To: CCL Subject: CCL: Dacapo Message-Id: <-33000-061110111954-18062-K0H6fmH09svLzZmAjboa7w]|[server.ccl.net> X-Original-From: davidofkozlowski Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Fri, 10 Nov 2006 16:20:13 +0100 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: davidofkozlowski [davidofkozlowski+/-gmail.com] Car-Parrinello Molecular Dynamics is a freeware code (but only for non profit organizations) available on this site http://www.cpmd.org/ cpmd_licence.html Le 10 nov. 06 à 15:34, Betty Coussens betty.coussens]=[dsm.com a écrit : > Sent to CCL by: "Betty Coussens" [betty.coussens * dsm.com] > Dear all, > > We would like to study the interaction of reasonably sized organic > molecules like di-n-butyl-phthalate with various surfaces of alpha > and beta MgCl2. We therefore want to implement a periodic plane > wave code on our PC cluster. Of course several commercial codes > are available such as CPMD, CASTEP etc. However, all of these > codes cost a lot of money. Looking on the internet and the > available literature it seems that a freeware code like Dacapo > might be a good choice as well. Can anybody comment on this? > > Thanks in advance! > > Betty > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Fri Nov 10 13:35:01 2006 From: "Deskins, Nathaniel A nathaniel.deskins%x%pnl.gov" To: CCL Subject: CCL: Dacapo Message-Id: <-33001-061110112116-20728-iBf92X4AFubLX7Dx+3n0BQ{=}server.ccl.net> X-Original-From: "Deskins, Nathaniel A" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 10 Nov 2006 07:21:01 -0800 MIME-Version: 1.0 Sent to CCL by: "Deskins, Nathaniel A" [nathaniel.deskins:+:pnl.gov] You may find this discussion from earlier this year useful. http://www.ccl.net/chemistry/resources/messages/2006/02/28.032-dir/index .html Aaron -----Original Message----- > From: owner-chemistry{}ccl.net [mailto:owner-chemistry{}ccl.net] Sent: Friday, November 10, 2006 6:30 AM To: Deskins, Nathaniel A Subject: CCL: Dacapo Sent to CCL by: "Betty Coussens" [betty.coussens * dsm.com] Dear all, We would like to study the interaction of reasonably sized organic molecules like di-n-butyl-phthalate with various surfaces of alpha and beta MgCl2. We therefore want to implement a periodic plane wave code on our PC cluster. Of course several commercial codes are available such as CPMD, CASTEP etc. However, all of these codes cost a lot of money. Looking on the internet and the available literature it seems that a freeware code like Dacapo might be a good choice as well. Can anybody comment on this? Thanks in advance! Betty From owner-chemistry@ccl.net Fri Nov 10 14:10:01 2006 From: "Alexander Yakovenko yakovenko_a]![ukr.net" To: CCL Subject: CCL: forces problem Message-Id: <-33002-061110125605-11570-ytYN9rCGH/VvO0KHajJZhA#server.ccl.net> X-Original-From: Alexander Yakovenko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 10 Nov 2006 21:23:24 +0200 MIME-Version: 1.0 Sent to CCL by: Alexander Yakovenko [yakovenko_a||ukr.net] Dear all, Does anybody have had the problems with gradient vector of bonded interactions? I am aimed to make energy minimization routine. The following problem appeared after simultaneous minimization of valence bonds and angles (with a bit modified MMFF94). The independent bonds and angles minimization shows an excellent convergence but their simultaneous processing fails at gradient of 10^2 kcal/A. The forces calculates as: F[i]=-F[j]=143.9325*K*(rij-r0)*(1-3*(rij-r0)+14/3*(rij-r0)^2) *r_ij/rij for bonds and Ka=0.043844*K*(a-a0)*(1-0.0105*(a-a0))/sqrt(1-cosA^2) F[i]=Ka*(r_kj/rij/rkj-cosA*r_ij/(rij^2)) F[j]=-F[i]-F[k] F[k]=Ka*(r_ij/rij/rkj-cosA*r_kj/(rkj^2)) for angles Where r_ij is a vector and rij is its length. The test problem is small (angles+bonds<100) and I do not know what is wrong here. That you a lot for any help. Best regards, ------------------------------------------- Alexander Yakovenko Zabolotnogo str 150 Institute of Molecular Biology and Genetics Kiev Ukraine From owner-chemistry@ccl.net Fri Nov 10 15:03:01 2006 From: "Dr. N. SUKUMAR nagams-#-rpi.edu" To: CCL Subject: CCL: difference between molecular modelling and molecular simulation Message-Id: <-33003-061110143018-12241-4bm8XK9cdcXkUxY/HZw0zw++server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 10 Nov 2006 14:30:11 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams]*[rpi.edu] On Fri, 10 Nov 2006 12:33:45 EST "srinivas raju g raju.g.srinivas^gmail.com" wrote: > Sent to CCL by: "srinivas raju g" [raju.g.srinivas,gmail.com] > hi, > i have just finished my Masters in chemistry and wish to take up computational chem. for research. i need little clarification in this regard. can someone explain the difference ( if any) between "molecular modelling" and "molecular simulation" . We discussed these issues in a recent review: Curt M. Breneman and N. Sukumar, "New Developments in Molecular Modeling" in the "Yearbook of Science and Technology" (McGraw-Hill, New York, 2004) If your library doesn't have access to this, email me directly; I can't post it on the list for copyright reasons. > as far as i know "molecular simulation" is generally associated with liquids and gases but "molecular modelling" is associated with proteins organic molecules etc. can anyone explain their differences ( in terms of what one does during research in these areas). how are these two different in terms of application to industry? For example, is molecular dynamics/simulation applicable to drug design? > regards, > srinivas raju.g We belive so. At RECCR (Rensselaer Exploratory Center for Cheminformatics Research), we are, among other things, developing molecular simulation-based descriptors that will be applicable to drug design. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Fri Nov 10 17:33:00 2006 From: "donna]_[dbkonline.com" To: CCL Subject: CCL: difference between molecular modelling and molecular simulation Message-Id: <-33004-061110170033-22661-ZpeyRKOH5aCGNWmIKGZCDg!A!server.ccl.net> X-Original-From: donna[*]dbkonline.com Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 10 Nov 2006 15:01:02 -0600 MIME-Version: 1.0 Sent to CCL by: donna-$-dbkonline.com Quoting "Dr. N. SUKUMAR nagams-#-rpi.edu" : > Sent to CCL by: "Dr. N. SUKUMAR" [nagams]*[rpi.edu] > On Fri, 10 Nov 2006 12:33:45 EST "srinivas raju g > raju.g.srinivas^gmail.com" wrote: > >> Sent to CCL by: "srinivas raju g" [raju.g.srinivas,gmail.com] >> hi, >> i have just finished my Masters in chemistry and wish to take up > computational chem. for research. i need little clarification in this > regard. can someone explain the difference ( if any) between "molecular > modelling" and "molecular simulation" . > As someone who has done both - I would put the difference as a time/motion type thing. To me "modeling" would be a static model... a protein structure, a ligan conformation, a binding site, a polymer configuration etc. The "simulations" I have run - are time laspsed type things .. so folding a protein from ext chain (using NMR data) ... ligand docking into a protein active site ... permeation of small molecule through a membrane ... etc. Usually these are Molecular Dynamics or Monte Carlo calculations and represent a time lapse of the process being looked at. That's just how I wouls divide it anyway., Hope that helps Donna Donna Bassolino-Klimas, Ph.D. DBK Consulting, LLC