This is why I still don't understand. Best regards, Asaf ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Asaf Farhi [asaf.fa...@weizmann.ac.il] Sent: Wednesday, August 08, 2012 1:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Question about Thermodynamic Integration
Dear Justin Thank you very much for the reply. It's written in the manual: 5.7.4 Topologies for free energy calculations Free energy differences between two systems, A and B, can be calculated as described in sec. 3.12. Systems A and B are described by topologies consisting of the same number of molecules with the same number of atoms. Best regards, Asaf ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, August 08, 2012 1:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Question about Thermodynamic Integration On 8/8/12 3:11 AM, Asaf Farhi wrote: > Dear Gromacs users > > Hi. I wanted to ask about the use of Thermodynamic Integration. > If the two compared molecules have a different number of atoms (e.g > Theophylline and Methylxanithe) what should I do in order to simulate it well > (it's written that you have to have the same number of atoms)? > If by "comparing molecules" you mean you are evaluating differences in, e.g., hydration free energy, there is no such requirement. What I believe you are thinking of is a FEP transformation between different species, an in silico mutation process. In that case, one would use dummy atoms that are transformed into real interacting species over the course of the lambda-dependent transformation. In the case of TI, no such requirement exists. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
