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. Cheers, 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 8:07 AM Subject: Re: [gmx-users] GROMACS command for energy calculation On 27/08/2012 8:01 AM, Acoot Brett wrote: > Dear Justin, > > In the internet there is the following content. But if I need to measure the > non-bonded energy between residues within a protein, or between fragments > within a protein, can you advise on how to set up the energygrp? http://www.gromacs.org/Documentation/File_Formats/Index_File Mark > > Cheers, > > Acoot > Energy group exclusions > energygrp_excl: > Pairs of energy groups for which all non-bonded interactions are excluded. > An example: if you have two energy groups Protein and SOL, > specifying > energygrp_excl = Protein Protein SOL SOL > would give > only the non-bonded interactions between the protein and the solvent. This is > especially useful for speeding up energy calculations with mdrun -rerun and > for excluding interactions within frozen groups. > > > ----- 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 7:09 AM > Subject: Re: [gmx-users] GROMACS command for energy calculation > > > > On 8/26/12 5:02 PM, Acoot Brett wrote: >> Dear All, >> >> After the production MD has been done, does GROMACS has a command which can >> calculate the interaction energy between any 2 residues in a frame of >> structure from the MD? >> > Assuming you have made proper use of energygrps in the .mdp file, you can > extract nonbonded terms between these groups from the .edr file using > g_energy. If you have not set energygrps, you can create a new .tpr file and > use mdrun -rerun to recalculate the energies from an existing trajectory or > snapshot. > > -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
