[gmx-users] Pressure swings during preliminary runs
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 25 21:48:25 CEST 2009
Warren Gallin wrote:
> 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.
> On 25-Aug-09, at 1:23 PM, Justin A. Lemkul wrote:
>> Warren Gallin wrote:
>>> 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:
>> The behavior you are seeing is quite normal. See here:
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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