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
expected.
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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