[gmx-users] drift of simulation cell

[Qing Zhu]

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.

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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