[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:
> 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.


> 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


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