Warren Gallin wrote:
Justin,
OK, I see what's going on.
So then, since the instantaneous pressure values are so variable, is
there a reason to implement pressure coupling for an MD run?
I guess if you're skeptical, check out the references for the coupling
algorithms implemented in Gromacs. Pressure affects a number of other
observables, which, when averaged over time, represent the macroscopic
properties (density, membrane properties, etc). I've always found that, despite
the fluctuation, the average pressure is correct.
-Justin
Warren
On 25-Aug-09, at 1:23 PM, Justin A. Lemkul wrote:
Warren Gallin wrote:
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?
Defaults are applied by grompp; the mdout.mdp file will show all
default values if you haven't specified them. Otherwise, check out:
manual.gromacs.org
The behavior you are seeing is quite normal. See here:
http://oldwiki.gromacs.org/index.php/pressure
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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