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? 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
