Hi Mark, Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file?
Acoot ----- Original Message ----- From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, 27 August 2012 8:00 PM Subject: Re: [gmx-users] GROMACS command for energy calculation On 27/08/2012 7:42 PM, Acoot Brett wrote: > Dear Justin, > For example, I want to calculate the energy between residue 50 and residue >100, then I create an index file (A), then in the MDP file I will insert >energygryp=A (with indec file extension or not?), then do the rerun, am I >right? An index file *contains* definitions of index groups. You need an index file that defines every group you care about, and you refer to the names of those groups in your .mdp file. Mark > Cheers, > Acoot > > > ----- Original Message ----- > From: Justin Lemkul <jalem...@vt.edu> > To: Acoot Brett <acootbr...@yahoo.com>; Discussion list for GROMACS users > <gmx-users@gromacs.org> > Cc: > Sent: Monday, 27 August 2012 9:53 AM > Subject: Re: [gmx-users] GROMACS command for energy calculation > > > > On 8/26/12 7:44 PM, Acoot Brett wrote: >> Dear All, >> >> I am still confused and I hope I can get some detailed explaination. For >> example, I want to determine the interaction energy between residue 52 and >> residue 105, how should I set energyggryp and what is the related commands? >> >> And if I want to determine the interaction energy between residue 52 in >> China A and residue 8 in Chain B, what will be the difference? >> >> You can also tell me a internet link on it. >> > The help information from make_ndx is what you need. Type "help" at the > prompt > (without quotes) and you will see examples. > > For instance, to select residue 52 of chain A: > > ch A & r 52 > > That creates a group that you can then use as an energygrp in the .mdp file. > > -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
