[gmx-users] problem with npt

[Xavier Periole]

On Tue, 4 Dec 2007 05:56:22 +0000
  pragya chohan <pragyachohan at hotmail.com> wrote:
> 
> Dear users
> I was tyring to run an npt simulation of membrane. My mdp is:

The changes you observe are not dramatic. Why this seems a problem
to you?
I could not find the actual values of cut-off for vdw interactions.

XAvier

> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 50000 ; total 100 ps.
> nstcomm = 1
> nstxout = 250
> nstenergy = 100
> nstlist = 10
> ns_type = grid
> pbc = xyz
> coulombtype = PME
> vdwtype = cut-off
> ; Berendsen temperature coupling is on in two groups
> ; aniisotropic pressure coupling is now on
> Tcoupl = berendsen
> Pcoupl = Parrinello-Rahman
> pcoupltype = semiisotropic
> tc-grps = POPC SOL
> tau_t = 0.1 0.1
> ref_t = 300 300
> ref_p = 1 1
> tau_p = 10
> compressibility = 4.5e-5 4.5e-5
> ; Energy monitoring
> energygrps = POPC SOL
> ; Generate velocites is off at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
> comm_grps = POPC SOL
> 
> 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.
> 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.
> _________________________________________________________________
> Post free property ads on Yello Classifieds now! www.yello.in
> http://ss1.richmedia.in/recurl.asp?pid=220

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------