[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 25 23:00:53 CET 2011


On 26/01/2011 12:05 AM, Justin A. Lemkul wrote:
>
>
> gromacs wrote:
>> HI Friends,
>>
>> I get the following note,
>>
>> The Berendsen thermostat does not generate the correct kinetic energy
>>   distribution. You might want to consider using the V-rescale 
>> thermostat.
>>
>> I want to keep the T at 300K, so does it matter to select any 
>> thermostat method?
>>
>
> The choice of thermostat certainly does matter, otherwise you wouldn't 
> get this note.  Refer to the numerous discussions in the list archive 
> as to why one would or would not (usually) use the Berendsen 
> thermostat, as well as:
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
> http://www.gromacs.org/Documentation/Terminology/Berendsen

... and the relevant manual sections.

Mark

>
>>
>> Another note when i use PME:
>>
>> Estimate for the relative computational load of the PME mesh part: 0.97
>>
>> NOTE 1 [file aminoacids.dat, line 1]:
>>   The optimal PME mesh load for parallel simulations is below 0.5
>>   and for highly parallel simulations between 0.25 and 0.33,
>>   for higher performance, increase the cut-off and the PME grid spacing
>>
>> So what is the reason? I use type=PME
>>
>
> Your combination of settings (rcoulomb, fourierspacing, and perhaps a 
> few others) indicate that your simulation is going to spend an 
> inordinate amount of time doing PME calculations, so your performance 
> will suffer.  Seeing your entire .mdp file would be necessary if you 
> want further guidance.
>
> -Justin
>
>> Is my setting proper?
>>
>> Thanks
>>
>>
>




More information about the gromacs.org_gmx-users mailing list