[gmx-users] drift of simulation cell

[David van der Spoel]

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.
Use g_traj

> 
> 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?
> 
> Thanks
> 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.
>>
>>> Thanks
>>>
>>> Qing Zhu
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>>
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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://folding.bmc.uu.se
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