[gmx-users] COM motion removal problem
K.A. Feenstra
Feenstra at chem.vu.nl
Wed Oct 16 09:54:11 CEST 2002
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 |
| |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
| |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
| / \ |-----------------------------------------------------------|
| ( ) | Dept. of Biophysical Chemistry - University of Groningen |
| \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
| __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
| / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
| ( ) |-----------------------------------------------------------|
| \__/ | "If You See Me Getting High, Knock Me Down" |
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