David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 5 16:19:45 CEST 2005
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 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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