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

Priyesh Mohanty priyeshmohanty at yahoo.in
Thu Apr 20 15:18:53 CEST 2017

Dear Justin and Chris,There appears to be no difference between the old and the newly created .tpr files. I determined this using gmxcheck. As an additional confirmation I reperformed a production simulation of Ubiquitin using the old .tpr which originally gave the proper occupancies for a given salt bridge. The reperformed run also shows the increase in occupancy compared to the original run. I think this suggests a problem with mdrun. This problem appeared simultaneously across across multiple machines. The stability is more than three times higher in the newer run with the same corrections (53% vs 16% occupancy using a 5 angstrom cutoff). 


    On Monday, 17 April 2017 7:33 PM, Priyesh Mohanty <priyeshmohanty at yahoo.in> wrote:

 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. 


    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 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

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