[gmx-users] problem in NPT equilibration step

srinathchowdary srinathchowdary at gmail.com
Mon Oct 14 16:32:22 CEST 2013

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

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
> --
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V.Srinath Chowdary

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