[gmx-users] Pressure swings during preliminary runs

Warren Gallin wgallin at ualberta.ca
Tue Aug 25 21:36:52 CEST 2009


	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?


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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