From: Jacob Poehlsgaard (jacobp_at_bmb.sdu.dk)
Date: Wed Apr 19 2006 - 04:03:53 CDT
> I guess it is feasible to use VMD and SMD to do this type of
> 1. separate the part you are interested into a different
> file, and let NAMD calculate all the forces.
> 2. From the parts you are interested in, use tcl force to
> calculate all the forces you needed from the frozen parts
> (the electrostatic contri).
> 3. Add these tcl forces to the first part.
> Thus, this is similar to SMD. I do not have any sample script
> to do this directly. But I think the VMD gurus out there will
> be able to help you achieve the above -- if you like the idea.
Wow, that's a really elegant solution. Perhaps I'd better include a small
shell of fixed atoms in the actual run to avoid any transition weirdness?
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