Berendsen has the right average volume, but not the right distribution of volumes.
http://pubs.acs.org/doi/abs/10.1021/ct300688p Did you equilibrate berendsen until the volume stabilized and THEN switch to parrinello-rahman for production? That's the suggested thing to do. On Fri, May 16, 2014 at 5:25 PM, Nilesh Dhumal <ndhu...@andrew.cmu.edu>wrote: > One initial structure is equilibrated for 10ns using Gromacs VERSION > 4.0.7. If I run same structure with same .mdp and same force field > parameters using gromacs VERSION 4.5.5. I got the error system is > blowing up. > I made another new initial structure which is not equilibrated and I got > the same error. After changing pressure coupling from parrinello-rahman to > berendsen , both the simulations went well. > > Nilesh > > > > Unstable models or unstable initial conditions will behave unpredictably. > > Unfortunately you've not given us much to go on. > > > > Mark > > On May 16, 2014 6:08 PM, "Nilesh Dhumal" <ndhu...@andrew.cmu.edu> wrote: > > > >> > > >> > > >> > On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: > >> >> Hello, > >> >> > >> >> I am running the simulation for ionic liquids. I initially did > >> >> simulation > >> >> with Gromacs VERSION 4.0.7 with "parrinello-rahman" pressure > >> coupling. > >> >> Here I pasted temperature and pressure coupling part of mdp file. > >> >> > >> >> ; Temperature coupling is on > >> >> Tcoupl = v-rescale > >> >> tau_t = 0.1 > >> >> tc-grps =system > >> >> ref_t = 350 > >> >> ; Pressure coupling is on > >> >> Pcoupl = parrinello-rahman > >> >> pcoupltype = isotropic > >> >> tau_p = 0.5 > >> >> compressibility = 4.5e-5 > >> >> ref_p = 1.0 > >> >> > >> >> We updated gromacs version to recent Gromacs VERSION 4.5.5. With > >> these > >> >> parameter during equilibration, I got the error "system is blowing > >> up". > >> >> I > >> >> changed "parrinello-rahman" pressure coupling to berendsen and able > >> to > >> >> run > >> >> the simulation. > >> >> > >> >> ; Temperature coupling is on > >> >> ;Tcoupl = Nose-Hoover > >> >> tau_t = 1.0 > >> >> tc-grps =system > >> >> ref_t = 400.0 > >> >> ; Pressure coupling is on > >> >> Pcoupl = berendsen; parrinello-rahman > >> >> pcoupltype = isotropic > >> >> tau_p = 0.5 > >> >> compressibility = 4.5e-5 > >> >> ref_p = 1.0 > >> >> > >> >> Is there any changes in recent version in pressure coupling? > >> >> > >> > > >> > Is there any prior equilibration? Using P-R for the initial phase of > >> > equilibration can be unstable. 4.0.7 was a bit more forgiving, and > >> this > >> > same > >> > issue has been reported several times before with the 4.5.x series, > >> with > >> > the > >> > solution being to set nstpcouple = 1 for the initial phase of > >> > equilibration with > >> > P-R. > >> > >> I did the simulations for two different initial structure. > >> 1. Pre-equilibrated 2. New initial structure. > >> > >> Nilesh > >> > >> > > >> > -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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