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

Justin Lemkul jalemkul at vt.edu
Mon Apr 17 13:42:15 CEST 2017

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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