From: John Stone (
Date: Wed Nov 26 2014 - 16:51:32 CST

  This kind of question falls into the domain of the particular
MD simulation tool you're using, and asking that program to save
the velocities or forces in a trajectory file. VMD doesn't have
the ability to compute these values, so if they aren't available
in a trajectory, then there's really no way to compute them
after-the-fact, at least in VMD. You might be able to feed a
simulation trajectory into an MD engine as input and have it
compute the quantities of interest, but again, this is totally
outside the scope of VMD currently.

  John Stone

On Mon, Nov 24, 2014 at 09:29:50AM +0800, sunyeping wrote:
> Dear all,
> Do you have an idea how to monitor the velocity of the water molecules
> that interact with a particular residues of the protein of the force that
> these water impose on that residue in the protein in a MD simulation
> trajectory?
> Thanks in advance.
> Yeping Sun
> Institute of Microbiology, Chinese Academy of Sciences

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