http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and http://www.gromacs.org/Documentation/Terminology/Pressure are useful here.
Mark On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary <srinathchowd...@gmail.com>wrote: > The barostat tries to equilibrate the system at the desired pressure, there > will be fluctuations and these fluctuations are little higher for > Parrinello-rahman if started far away from equilibrium value. I would > suggest to start from berendsen and then extend it to P-R. Also, you should > run little longer time for the system to reach equilibrium > regards > sri > > > On Mon, Oct 14, 2013 at 9:13 AM, Preeti Choudhary < > preetichoudhary18111...@gmail.com> wrote: > > > Dear Gromacs user, > > > > I am trying to simulate a protein (nmr structure).I have successfully > done > > energy minimisation step.Also I have equilibrated the system a 298 k > (which > > is achieved from 100 ps run) .Now,I am trying to equilibrate the system > at > > 1 bar pressure.After a run of 100 ps ,I am getting average pressure of > the > > system as 4.9 bar.Then I extended this simulation for 50 ps(total 150 ps > > from start) ,so the av. pressure dropped to 1.5 bar.Then,I again extended > > this simulation for further 50 ps(Total 200 ps from start),pressure > raised > > to 2.14 bar.Again ,I extended this simulation for further 50 ps(Total 250 > > ps),pressure raised to 3.56 bar.Similarly,it av. pressure is 2.98 > bar,2.85 > > bar,2.41 bar for 300ps, 350 ps and 400 ps.I am not able to equilibrate > the > > system at 1 bar pressure.What should be done in these cases? > > > > I am using opls-aa force field,tip-4 water model,for pressure coupling I > am > > using following parameters: > > ; Pressure coupling is on > > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > > pcoupltype = isotropic ; uniform scaling of box vectors > > tau_p = 2.0 ; time constant, in ps > > ref_p = 1.0 ; reference pressure, in bar > > compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 > > refcoord_scaling = com > > > > note :the initial pressure at the beginning of npt simulation and at the > > end of nvt simuation is -311.41 bar > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > V.Srinath Chowdary > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
