Computation of Pres-XX like terms for the selection SOL

User discussions
1

GROMACS version: 2021
GROMACS modification: No

I am interested in computing the solvent’s viscosity in a protein+water system. Therefore, I require the Pres-XX like terms which one typically extracts using gmx energy on the .edr file. However, I am unsure whether the Pres-XX and similar terms shown as options of gmx energy command are computed considering the whole system. If so, please let me know the correct procedure to get these terms only for the solvent.

I have tried gmx mdrun with -rerun as well using the SOL index file and setting energy-grps = SOL in my .mdp file. However, the resultant .edr file does not provide Pres-XX like options when run with gmx energy.

Even a new mdrun using the energy-grps = SOL in .mdp file does not seem to provide Pres-XX like terms specific to the SOL group.

Any suggestions will be highly appreciated.

Thanks,
Pallab

2

The pressure is a global property, there is no pressure for a subset of the system.

3

Thanks for your response.

I agree with your point. However, I was wondering if a partial pressure could be computed for a subset of the system.

4

That is not possible in GROMACS.

5

Thank you for your reply.