[gmx-users] problem in NPT equilibration step

[Mark Abraham]

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
<srinathchowdary at 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 <
> preetichoudhary18111989 at 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 at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> V.Srinath Chowdary
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>