HI,
I am trying to simulate the behavior of short peptides in an aqueous
solution.
When I look at the log of the progress of initial minimization runs
and longer production runs I am seeing crazy variations in the
pressure, including negative values and positive values well into the
100's of bar.
The temperature is equilibrating and stable, so I am thinking that I
have missed some salient feature of the barostat.
In one case I am not setting any of the relevant barostat parameters,
relying on the default values to work - is there someplace where i can
find waht the defaults values would be?
In another case I am using the following settings in the .mdp file:
integrator = md
nsteps = 50000
dt = 0.002
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
tcoupl = v-rescale
tc-grps = protein non-protein
tau-t = 0.1 0.1
ref-t = 298 298
Pcoupl = Berendsen
tau-p = 1.0
compressibility = 1e-5 1e-5 1e-5 0 0 0
ref-p = 1.0
nstenergy = 100
define = -DPOSRES
Can someone point me at some relevant information on how to
troubleshoot large rapid pressure variations?
Thanks
Warren Gallin
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