[gmx-users] Barostat & Density decreasing to zero
Omer Markovitch
omermar at gmail.com
Wed Feb 11 14:16:36 CET 2009
Dear All,
I have simulated a protein inside a box with water and ions. I began by
minimizing my system (which has a total charge of zero), until the maximum
gradient was small enough and the potential energy become negative.
Then I heated it, slowly, to 300K at constant volume (using berendsen
thermostat and tcoupl = 1 ps).
Then I performed 500 ps NVT simulation to equilibrate the temperature, at
300K.
Then, I tried to equilibrate the pressure and run NPT simulation, using
Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl
= 0.1).
My problem is, that with the barostat & thermostat both active in the same
MD run, my density drops to a very low value (at the first MD steps, the
density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions
increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the
pressure coupling constant, the speed of the expansion changes but all
simulation converged to a small density between 50-100 kg/m3.
Your help is appreciated; Probably, I am not controlling the simulation like
I should. I will appreciate any advice.
Thank you, Omer Markovitch.
I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run:
integrator = md
dt = 0.001
nsteps = 500000
comm_grps = system
nstxout = 500
nstvout = 500
nstcheckpoint = 1000
nstlog = 500
nstenergy = 500
nstlist = 10
ns_type = simple
pbc = xyz
rlist = 1.0
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
epsilon_r = 80
epsilon_rf = 80
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.0
table-extension = 1
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes
tcoupl = berendsen
tc-grps = system
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
Pcoupltype = Isotropic
tau-p = 10
compressibility = 4.5E-5
ref-p = 1
andersen_seed = 815131
constraints = none
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