[gmx-users] problem in NPT equilibration step

Preeti Choudhary preetichoudhary18111989 at gmail.com
Mon Oct 14 15:13:17 CEST 2013

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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