[gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

[Christopher Neale]

Just to list the ways that such a thing could happen:

1. change to $GMXLIB
2. change to the version of gromacs you are using or just a change to a different installation (so you have a different top directory)
3. you automate grompp by piping in a number and some change to #1 or #2 above has affected that number so that you are no longer getting the forcefield you desire.

-- You should be able to run gmx dump -s new.tpr > z to figure out what sigma you are getting now, or you could compare with gmx check -s1 old.tpr -s2 new.tpr ... this would at least tell you if it's a change in the .tpr file.

Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Priyesh Mohanty <priyeshmohanty at yahoo.in>
Sent: 17 April 2017 10:03:14
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

Well, yes. I have been preparing .tpr files in the exact same way for the last 6 months or so when I was getting the correct occupancies with these corrections. There were no errors whatsoever.  In fact, when I delete the non-bonded salt bridge corrections from ffnonbonded.itp, I get considerably stronger salt bridges as one would expect from this particular forcefield. Hence, I really don't understand how grompp would suddenly start messing up when it comes to reading the topology file. The salt bridges occupancies that I get as of now are essentially stronger than they used to be but nowhere near as strong as they are without the corrections. This subtle increase however appears to considerably alter the dynamics for some multidomain proteins for which I previously performed simulations with these corrections.

-Priyesh



    On Monday, 17 April 2017 5:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:




On 4/17/17 6:09 AM, Priyesh Mohanty wrote:
> I've also tried increasing the sigma to higher values beyond 0.325 which should in principle considerably weaken salt bridges but there appears to be no decrease in salt bridge occupancy despite the increase in sigma. It is as though mdrun is not reading the nonbonded_param addition correctly.
>

mdrun doesn't read these files at all; grompp does when building your .tpr.  So
if you're making adjustments to ffnonbonded.itp after writing a .tpr file, there
will be no effect on the simulation because you haven't actually changed the
physical model.  Are you correctly re-creating the .tpr file each time?

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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