[gmx-users] VCM

[David van der Spoel]

On Tue, 2005-04-05 at 16:06 +0200, 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?  
I would suggest making just two groups (membrane and solvent), although
some people have used a third group for membrane protein which may
diffuse as a whole. Then try starting with an energy minimized
conformation and zero velocities. 
> 
>  
> 
>  
> 
> >> ; 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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