[gmx-users] how to output intramolecular pair interaction parameters

Smith, Micholas D. smithmd at ornl.gov
Thu Nov 16 18:53:18 CET 2017

You could use an energy group exclusion and then perform gmx mdrun -rerun where all of the pairs you aren't interested in are excluded from the energy calculation.

>From the manual:

    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. 

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Srinivasa Ramisetti <S.B.Ramisetti at leeds.ac.uk>
Sent: Thursday, November 16, 2017 12:48 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] how to output intramolecular pair interaction parameters

Hi all,

I would like to know if there is any way to output intramolecular pair interaction parameters that are generated by gromacs.

Thank you,

Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list