[gmx-users] drift of simulation cell
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 8 00:00:51 CEST 2006
Qing Zhu wrote:
> Hi All,
> I am using gromacs to simulate a lipid/cholesterol mixed membrane. When
> I looked at the trajectory using VMD, the whole simulation cell
> laterally drifted very fast, and it looked like center of mass motion.
> But when I set up the simulation, I did turn off the center of mass
> motion. I don't know where this drifting motion came from, and it had
> huge influence on the calculations of system diffusion property. So does
> anyone know how to remove this kind of fast drifting motion from the
> trajectory so that I can do some correct calculations on diffusion.
you want to turn off center of mass motion for membrane and water
separately. If you look closer you will probaböy see they move in
> Qing Zhu
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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://folding.bmc.uu.se
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