[gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

[Justin Lemkul]

On 3/24/20 3:09 AM, Wesley Michaels wrote:
> Hi,
>
> Thanks for your reply! I built the topology with my own script, as opposed
> to using pdb2gmx. Following Bogdan's instructions here (
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html),
> I specified all instances of 1-4 pair interactions (i.e. pairs of atom
> indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ]
> section (i.e. the interaction parameters for pairs of atom types)
> automatically using "gen_pairs" = "yes".
>
> As a second test, I generated a topology using pdb2gmx and the procedure
> Justin detailed here (
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html)
> (using the OPLS-AA FF option in pdb2gmx) and used that in a trial
> simulation. I experienced the same issue, unfortunately. Happy to provide
> any files as needed to help clarify the issue.

If pdb2gmx built the topology and you're using an unaltered 
forcefield.itp [defaults] directive, based on what you've said below, it 
appears to just be an equilibration issue. Use Berendsen for a while to 
get the system settled and then switch to Parrinello-Rahman. If you're 
still experiencing problems, full .mdp file(s) would be helpful.

-Justin

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Justin A. Lemkul, Ph.D.
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