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remove translation
#20313 03/02/09 05:18 PM
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dear charmmer,
my system (whole system) was drift during the simulation. is it possible to subtract the movement by its center of gravity from each snapshot of trajectory to make analysis of diffusion?

Thank you

Re: remove translation
beginner #20314 03/02/09 05:23 PM
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The merge command (dynamc.doc) can remove translation (merge orient norot).


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: remove translation
lennart #20315 03/02/09 06:15 PM
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It is not appropriate to remove translation when the goal is to calculate diffusion.

Re: remove translation
rmv #20316 03/02/09 06:45 PM
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It depends, and we don't really have enough information in this case. If the whole system (non-PBC) is moving systematically I'd say it would be OK to remove this overall translation to avoid having this contaminate the MSD calculation.


Lennart Nilsson
Karolinska Institutet
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Re: remove translation
lennart #20317 03/02/09 07:12 PM
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It is true that I was thinking about cases with PBC.

Re: remove translation
lennart #20318 03/02/09 10:34 PM
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Dear Dr. Nilson and rick

thank you very much for your support.

Actually, my system was simulated under PBC and it is a bilayer system. I observed some of lipids move out of the box, which I expect it should be no problem under PBC. After I combined the trajectory(merge trj), I observed the lipids were recentered in the PBC box, but whole system slightly drift (visualized by vmd)during the period of MD. I assumed that it may be due to wrong removal of center of mass correction. Such that, the diffusion coefficient for my system is very large.
I think perhaps I might need to subtracts the movement of system with certain value. Any comments would be appreciated.

Re: remove translation
beginner #20319 03/03/09 12:51 AM
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Lipids moving out of the box may or may not be a problem, depending on the details of the CRYStal and IMAGe centering setup during the simulation.

The MERGe command should not do any RECEntering unless told to do so.

The coordinates used to compute <r^2> vs. t for diffusion must be continuous, with no large jumps; you should verify that, perhaps by plotting some coordinate time series.

Re: remove translation
rmv #20320 03/03/09 04:03 PM
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Dear rick,

thank you very much.
May I ask another question? Is it possible to remove the center of gravity (of the system) from the trajectory?

Re: remove translation
beginner #20321 03/03/09 05:57 PM
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Perhaps, but how are you going to compute that for each frame? The center of mass would change upon image centering for one thing. Also, the result cannot be used to compute diffusion.


Moderated by  lennart, rmv 

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