[gmx-users] Dubious results with NPT

Justin Lemkul jalemkul at vt.edu
Mon Feb 24 17:06:08 CET 2014

On 2/23/14, 11:37 PM, sujithkakkat . wrote:
> Hello,
>    Thank you both for  the comments. I am using gromos96 forcefield . I read
> a little bit  and as you said the nonbonded cutoff has to be higher.
> The tau_p=5ps was chosen , since the manual mentions that the value has to
> be raised by 4-5 times on going from berendsen to parrinello-rahman
> barostat, though I did not completely follow the reasons behind it. I will
> try with lower values.
>     I had run an earlier simulation with the same parameters for a pure
> water system for 5ns and reference pressure 5bar, and things worked fine
> there with the average pressure at 5.15bar. I guess the sigma  for the case
> of water was low and therefore the small cut-off of 0.8nm did not matter.
> However the case of cyclohexane alone remains to be tried.
> I guess Dr Vitaly was saying about using a switch/shift function.
> I will try the simulation with the new settings and see.

The Gromos force fields were parametrized with a plain cutoff for van der Waals. 
  They do not require switching or shifting.  It's true that plain cutoffs are a 
bit harsh, but switching and shifting have their own issues, and one should 
always stick to the parametrization methods unless there is demonstrable 
evidence that the new method is better.  I have never known Gromos96 force 
fields to need anything other than plain cutoff for van der Waals to function as 



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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