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

[S. Joseph]

>
> 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?
The paper is Nanotechnology vol 19 (2008) 195702.

-Joseph