[gmx-users] how to keep the simulation box during simulation
Itamar Kass
ikass at cc.huji.ac.il
Tue Dec 16 14:03:00 CET 2003
Hi all, I am trying to simulate a lipid bilayer (at plain XY, such that it is normal to Z) with water at the two sides. When I do PR dynamics, using:
title = DMPC bi-layer solvated in water and Na ions.
cpp = /usr/bin/cpp
integrator = md
dt = 0.002
nsteps = 50000
; Constrain control
define = -DPOSRES
constraints = all-bonds
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 500
nstvout = 500
nstfout = 500
; nblist update frequency
nstlist = 10
; ns algorithm
ns_type = grid
rlist = 1.3
coulombtype = PME
rcoulomb = 1.3
rvdw = 1.3
fourierspacing = 0.10
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = Solvent DMPC
ref_t = 310 310
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 2 2
compressibility = 4.5e-5 0
ref_p = 1.0 1.0
; Generate velocites is on at 310 K.
gen_vel = yes
gen_temp = 310
; Electric field - used
; 100mV/3nm*10E-3v/mV = 0.033
E_z = 1 0.033 0.0
; Energy monitoring
energygrps = SOL DMPC
; Center of mass control
nstcomm = 1
comm-grps = Solvent DMPC
I got from the mdrun a box with different size then the one entered. I know I used pressure coupling, which might change the box, but the bilayer is ruined. I saw in articles (e.g. Biophys J. 2002 Jun;82(6):2934-42.) that it is possible to allow changes only at the z axis, how this is done? Does working this way, will keep the bilayer and it's properties physically?
And a second question if I may, when running gromacs, is it better to give to any CPU more then one job. For instance, if I have two CPU is it more efficient to cut the job into four parallel processes?
Thanks you all, Itamar.
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