[gmx-users] problem with npt
pragyachohan at hotmail.com
Fri Dec 14 19:32:37 CET 2007
thanks for your help.
My system ran fine for 250 ps but later the bilayer deformed very much.
my mdp is
integrator = md
dt = 0.002 ; ps !
nsteps = 125000 ; total 100 ps.
nstcomm = 1
nstxout = 250
nstenergy = 100
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 0.9
rlist = 0.9
; Berendsen temperature coupling is on in two groups
; aniisotropic pressure coupling is now on
Tcoupl = nose-hoover
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tc-grps = POPC SOL
tau_t = 0.5 0.5
ref_t = 323 323
ref_p = 1 1
tau_p = 10 10
compressibility = 4.5e-5 4.5e-5
; Energy monitoring
energygrps = POPC SOL
Can anyone help?
> Date: Wed, 5 Dec 2007 11:27:40 +1100
> Subject: Re: [gmx-users] problem with npt
> From: mark.abraham at anu.edu.au
> To: gmx-users at gromacs.org
> > Dear users
> > I was tyring to run an npt simulation of membrane. My mdp is:
> > As advised in a recent workshop on http://www.csc.fi/chem/course/gmx2007/
> > i am using Parrinello-Rahman instead of berendsen. The problem is that the
> > box size is getting reduced to 9.99448 9.99448 9.25077 from 10.0 10.0 10.0
> > and water is compressing the bilayer.
> This is the purpose of equilibration with NPT - to fix density issues. The
> contraction in Z suggests that your membrane is insufficiently dense in
> that direction, or has some vacuum pockets. That's not a problem in itself
> so long as you equilibrate long enough. Berendsen P-coupling will likely
> do the same thing.
> > I also tried anisotropic coupling
> > pcoupltype = anisotropic
> > tc-grps = POPC SOL
> > tau_t = 0.1 0.1
> > ref_t = 300 300
> > ref_p = 1 1 1 0 0 0
> > tau_p = 10
> > compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
> > This time my box size is reducing to 9.99065 9.99717 9.17646.
> > I cant figure out the problem. Any help will be appreciated.
> This suggests the same non-problem exists.
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