[gmx-users] parameters problem

Justin Lemkul jalemkul at vt.edu
Mon Mar 10 10:44:45 CET 2014

On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
> Thank you Mark and Justin.
> Now, I have carried out simulations using PME electrostatics and using all other
> parameters (except gromos 96 43a1 ff used) as suggested in
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
> The protein is not loosing its structure now. But the problem is if I carry out
> simulations in the presence of experimentally known stabiliser generated using
> ProDrg (keeping all the parameters same while simulating both in the presence
> and absence of stabiliser), the partial loss of secondary structure is observed
> in the presence of stabilizer relative to the case in its absence at 350K
> thereby implying simulations going against experimental observations (although
> slight stabilization was observed at 300K). Simulations were repeated twice with
> two different force fields.
> However if I use above em,pr,full parameters with cut-off electrostatics,
> although secondary structure is lost in the initial stages but I could clearly
> see the stabilization behaviour of additive in terms of secondary structure
> retainment till longer time. Is this observation a matter of chance- reliable or
> not? What could be the possible reason for not observing such stabilization with
> better parameters?

Cutoff electrostatics are horribly inaccurate.  The fact that you conveniently 
see what you hope to when using a plain cutoff is likely by chance.

The bigger issue is the use of PRODRG parameters.  As I have said numerous times 
on this list, the parameters it produces are demonstrably inaccurate and require 




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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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