[gmx-users] Pressure swings during preliminary runs

[Warren Gallin]

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?

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