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
