[gmx-users] VCM

[Erik Lindahl]

Hi,

I would simply use one "membrane" and one "water+ion" group for the 
VCM, since these molecules are separated in z-direction and thus can 
move in opposite directions due to the PBC. If you do VCM separately 
for each lipid type you might have problems equilibrating them, 
particularly if there is only a small number of some lipid.

The same goes for the Na ions - if you only have a handful of them they 
won't be able to move much if they form a separate VCM group.

(Note that you can define arbitrary groups either by using make_ndx or 
by hacking the index file manually)

Cheers,

Erik




On Apr 5, 2005, at 4:06 PM, Michal Kolinski wrote:

> Thank you for your comments.   I’m using  center of mass motion 
> removal for each lipid (PE PS PC) and for solvent. I guess it should 
> remove VCM of these groups, is there anything else I could do?  
>
>  
>
>  
>
> >> ; Groups for center of mass motion removal
> >> comm-grps            = PC  PE PS   SOL Na
> >> ; Mode for center of mass motion removal
> >> comm-mode            =  Linear
> >> ; Center of mass control
> >> nstcomm              =  1
>  
>  
>
>  
>
> How can I couple the membrane and the solvent separately?
>  
>  
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl              =  berendsen
> > tc-grps             =  PC  PE PS   SOL Na
> > tau_t               =  0.1   0.1   0.1  0.1 0.1
> > ref_t               =  310 310 310 310 310
> > ; Energy monitoring
> > energygrps          = PC  PE PS   SOL Na
> > ; Isotropic pressure coupling is now on
> > Pcoupl              =  berendsen
> > Pcoupltype          = semiisotropic
> > tau_p               =    20         20
> > compressibility     =  4.5e-5    4.5e-5
> > ref_p               =  1.0  1.0
>  
> Thank you for help!
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