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

[Srinivasa Ramisetti]

Hi Micholas,


Thanks for your reply. I tried as you suggested and could not find the information on pair interaction parameters.


I will try to rephrase my question so that it is clear to everyone. I have a list of intramolecular interactions between atoms in a molecule within the [ pairs ] section for which I believe gromacs generates the LJ C6 and C12 values when the gen-pairs is set to yes. So I want to know if there is any way to output/write the C6 and C12 values generated by gromacs to screen/file.


Thank you,

Srinivasa

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Smith, Micholas D. <smithmd at ornl.gov>
Sent: 16 November 2017 17:53:10
To: gromacs.org_gmx-users at maillist.sys.kth.se; gmx-users at gromacs.org
Subject: Re: [gmx-users] how to output intramolecular pair interaction parameters

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:


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.

===================
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,

Srinivasa
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