From owner-chemistry@ccl.net Tue Sep 18 08:44:00 2012 From: "Gkourmpis, Thomas Thomas.Gkourmpis,borealisgroup.com" To: CCL Subject: CCL: Looking for MD program to model droplets Message-Id: <-47617-120918035350-16702-v8h6GpsYiuSSHwf9IwvNZQ^server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 18 Sep 2012 09:53:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis*borealisgroup.com] Peeter Hi There are a number of really capable MD software packages available that can be parallelised and offer a wide range of capabilities. If you are looking for open licence software LAMMPS or NAMD are pretty good and able to handle large number of atoms. LAMMPS doesn't have a full pre/post processing GUI so you will need to arrange for one. One option is MAPS from a company called Scienomics that offers these capabilities. NAMD has a GUI (it is called VMD) but MAPS can also be used to setup and analyse jobs without too much trouble. If you want to get a fully commercial package (MD code and GUI integrated together) then probably check what Accelrys offers, as they have a wide range of software packages for specific applications. Here are the relevant web pages for you to check what is most appropriate for your needs LAMMPS http://lammps.sandia.gov/ NAMD http://www.ks.uiuc.edu/Research/namd/ VMD http://www.ks.uiuc.edu/Research/vmd/ Scienomics http://scienomics.com/ Accelrys http://accelrys.com/ I hope this helps but if you need any more help/information give us a shout Thomas Dr Thomas Gkourmpis Researcher - Innovation & Technology Borealis AB | SE-444 86 Stenungsund | Sweden Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 www.borealisgroup.com | 556078-6633 | Swedish Companies Registration Office ___________________________________ Borealis - Shaping the Future with Plastics -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com..ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com..ccl.net] On Behalf Of Peeter Burk peeter|a|chem.ut.ee Sent: Tuesday, September 18, 2012 8:15 AM To: Gkourmpis, Thomas Subject: CCL: Looking for MD program to model droplets Sent to CCL by: "Peeter Burk" [peeter#,#chem.ut.ee] Dear colleagues, We are planning to extend our activities to the MD modeling of droplets in atmosphere. Could anyone suggest a suitable program, which can be used for MD modeling of water and also other solvent (e.g. acetonitrile, DMSO) droplets containing some organic solutes (neutral and also cationic or anionic forms). The program should be capable of handling droplet of several thousand molecules in a reasonable time. So far we have had some preliminary tries with tinker and amoeba force field with some success, but tinker seems not to be parallelized so I would like to inquire about other (faster, better, etc.) options. Best regards Peeter Burk University of Tartu, Estonia burk{=}ut.eehttp://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.