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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.