[gmx-users] COM motion removal problem

[K.A. Feenstra]

"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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