[gmx-users] drift of simulation cell
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 8 16:56:54 CEST 2006
Qing Zhu wrote:
> Thanks for the quick reply, but now the situation is we already finished
> a very long run before we realized this problem. So what I want to know
> is for the given trajectory we have now, can we correct it in
> retrospect, or if anything from the simulation might be salvaged.
you can do it with trjconv, but if a lot of motion has gone into the
center of mass motion of the water and/or membrane that means you have
simulated at a lower temperature than what you think you have. Compare
the kinetic energy of the membrane (from trr file) and from the center
of mass motion.
> When you said turning off the center of mass motion for membrane and
> water separately, is it to specify membrane and water separately instead
> of the whole system in "comm_grps" option?
> Qing Zhu
> David van der Spoel wrote:
>> 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
>> opposite directions.
>>> 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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