Re: Solute KE

From: Shantenu Jha (
Date: Thu Dec 04 2003 - 17:08:23 CST

> So although, I wasn't able to get the above approach working, using
> another trick (involving generating a pdb file with the solvent atoms beta
> value set to 1, and setting fixedAtoms parameter in my NAMD config file to
> be "on" and setting fixedAtomsfile to the generatd pdb file), I was able
> to get NAMD to spit out what appears to be solute only Kinetic Energies
> (based on it passing some basic consistency checks), and thus back to the
> first question, i.e. does NAMD 2.5 implement the ability to give KE/Temp
> for a subset of atoms and thus can the numbers I get from the above
> procedure be trusted?)

I should add that in this approach, I'm not using the "coorfile" command
to load dcd files, but but using the checkpoint (coor and vel) files.
Don't think its possible to load both a velocity dcd and coordinate dcd
using coorfile?


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