On Tue, 4 Dec 2007 05:56:22 +0000
pragya chohan <[EMAIL PROTECTED]> 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.
_________________________________________________________________
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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