No full solutions to this problem -- I'll write a few notes. * With large systems run for relatively small amounts of time, the ensemble could be statistically indistinguishble from the true distribution even if the averages don't line up correctly. See:
http://pubs.acs.org/doi/abs/10.1021/ct300688p For ways to examine the full distribution of volumes. * Parrinello-Rahman isn't quite correct in GROMACS because virial and kinetic energy are offset by 1/2 a step, though getting something more like 1.2 atm when running at 1 atm is more common. * Note that with systems that are heterogeneous in direction (not uniform in x y and z), any errors in the pressure may be magnified. * If you have a property that changes when the pressure changes from 1 to 5 atm, odds are that molecular simulation is not the right way to study it -- the force fields are not that accurate. On Tue, Feb 25, 2014 at 6:48 AM, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > in that case the average is reasonable, but you should state in the > manuscript that all the reported results correspond to 5.15 bar. > > > Dr. Vitaly V. Chaban > > > On Tue, Feb 25, 2014 at 10:42 AM, sujithkakkat . <sujithk...@gmail.com> wrote: >> Hi, >> >> In fact the average pressure 5.15 bar was obtained for the case where the >> reference pressure was 5 bar. I had mentioned it in one of the previous >> mails. But still the average value is not that good. >> >>>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. >> >> >> Sujith. >> >> >> On Tue, Feb 25, 2014 at 2:29 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> >> wrote: >>> >>> your average pressure is the pressure you should report in the >>> publication. if you got 5 bars instead of 1 bar, you should write >>> >>> "I simulated the system at 5 bars" >>> >>> >>> Dr. Vitaly V. Chaban >>> >>> >>> On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . <sujithk...@gmail.com> >>> wrote: >>> > On Mon, Feb 24, 2014 at 5:37 AM, sujithkakkat . <sujithk...@gmail.com> >>> > 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. >>> > >>> > >>> > No, this average pressure is not fine. >>> > >>> > >>> > >>> > Why isn't it fine? I admit it is not very good. I guess due to huge >>> > fluctuations the average pressure is tend to vary a bit to either side >>> > of >>> > the reference value, unless I continue the equilibration for a very long >>> > time. Also the average was calculated with g_energy, which I guess >>> > considered the entire simulation, where the first few time steps, when >>> > the >>> > system is away from equilibrium, would have poor pressure values with >>> > respect to reference , which would reflect in the average pressure >>> > calculated. >>> > Also using g_analyze to calculate average pressure between different >>> > times >>> > during the simulation did not give the same value. So I am not sure if >>> > I >>> > should aim at an average pressure which is equal to the reference >>> > pressure. >>> > >>> > Thanks, >>> > Sujith. >>> > >>> > >>> > >>> > On Mon, Feb 24, 2014 at 4:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >> >>> >> >>> >> >>> >> 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. >>> > >>> > >>> -- >>> 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. >> >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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