Hi Omer,
You use a dielectric constant is 80, which means that the electrostatic
interactions are screened. Perhaps that's why your density is low.
Ran.
Omer Markovitch wrote:
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 = 50
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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