[gmx-users] COM motion removal problem

[K.A. Feenstra]

Hi,

Sorry -- you can safely ignore my previous mail. I thought you were
removing rotation (which isn't necessary if you have a solvent-filled
box)... %-{

"K.A. Feenstra" wrote:
> 
> "Filip Ryjácek" wrote:
> >
> > Hi all,
> > I have got serious problem with my simulation (DNA with counterions solvated
> > in box of water). With the following settings GROMACS removed  C.O.M. motion
> > periodically, but...it looks strange. Every 10ps the total temperature falls
> > to 150K, but in 10ps is back again at 300K. See enclosed graphs (pdf
> > format).
> > I know molecules should diffuse, but the fluctuations in temperature seem
> > unnatural.
> >
> > ;
> > comm_grps           =  DNA Na+ SOL
> > nstcomm             =  10000 10000 10000
> > comm_mode           =  Linear
> 
> If I understand the current implementation correctly, this will remove
> the rotation of your DNA, ions and water, each one of them *independently*.
> Especially for the ions I could imagine this can have a big effect on
> their overal motion -- and hence on their temperature. Probably you would
> want to remove rotation of the whole system (group name "System"), or
> for the DNA only (name "DNA"). It would also depend on what groups you
> chose for temperature coupling. I would advise on coupling two groups:
> one "DNA" and one "Sol+Ions". I've seen many people couple ions separately,
> but IMHO that can give artefacts as well.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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