[gmx-developers] Re: gmx-developers Digest, Vol 59, Issue 7

[David van der Spoel]

S. Joseph wrote:
>> Can't it be that what you see is caused by the center of mass removal?
>> also i
>> What happens if you try without the oscillating field, but the identical
>> mdp parameters
>>
>> Gerrit
> 
> Thanks Gerrit and David, I did think about COM motion so I did not use
> specify nstcomm or comm_mode thinking that the default was no center
> of mass motion removal. Before posting to the list I had tried without
>  an oscilating field, and the particle had moved (albeit very slowly)
> for dc fields (for both my code as well as original code) for voltages
>  as small as 0.003 V/nm for single precision so I assumed the center
> of mass motion was not being removed and that the reason it did not
> move for smaller voltages was due to single precision.  I checked
> gmxdump today and saw that nstcomm was 1 if I didn't specify anything.
> I entered comm_mode as none and voila the particle started oscillating
>  as expected.
> 
> David, I did not use temperature coupling. Can I  use it for
> simulations with few particles?
I would try to avoid it if you can in the gas phase. You may need to use 
double precision to get good energy conservation. However if you apply 
an electric field to a charged molecule (or dipoles), you are doing work 
and the temperature will not be constant in general.


> The paper is Nanotechnology vol 19 (2008) 195702.
> 
> -Joseph
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se