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Hi Omer,<br>
You use a dielectric constant is 80, which means that the
electrostatic interactions are screened. Perhaps that's why your
density is low.<br>
Ran.<br>
<br>
Omer Markovitch wrote:
<blockquote
cite="mid8c3f24a40902110516m48e5214bs6df0c34ee0029f2f@mail.gmail.com"
type="cite">
<div dir="ltr">Dear All,<br>
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.<br>
Then I heated it, slowly, to 300K at constant volume (using berendsen
thermostat and tcoupl = 1 ps).<br>
Then I performed 500 ps NVT simulation to equilibrate the temperature,
at 300K.<br>
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).<br>
<br>
<div class="Ih2E3d">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.<br>
</div>
<div class="Ih2E3d"><br>
Your help is appreciated; Probably, I am not controlling the simulation
like I should. I will appreciate any advice.<br>
Thank you, Omer Markovitch.<br>
<br>
</div>
I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run:<br>
<br>
integrator = md<br>
dt = 0.001<br>
nsteps = 500000<br>
comm_grps = system<br>
nstxout = 500<br>
nstvout = 500<br>
nstcheckpoint = 1000<br>
nstlog = 500<br>
nstenergy = 500<br>
nstlist = 10<br>
ns_type = simple<br>
pbc = xyz<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb-switch = 0<br>
rcoulomb = 1.0<br>
epsilon_r = 80<br>
epsilon_rf = 80<br>
vdw-type = Cut-off<br>
rvdw-switch = 0<br>
rvdw = 1.0<br>
table-extension = 1<br>
fourierspacing = 0.12<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 3d<br>
optimize_fft = yes<br>
tcoupl = berendsen<br>
tc-grps = system<br>
tau_t = 0.1<br>
ref_t = 300<br>
Pcoupl = berendsen<br>
Pcoupltype = Isotropic<br>
tau-p = 10<br>
compressibility = 4.5E-5<br>
ref-p = 1<br>
andersen_seed = 815131<br>
constraints = none<br>
<br>
</div>
<pre wrap="">
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