RE: Computing cost of frozen atoms

From: Jacob Poehlsgaard (
Date: Wed Apr 19 2006 - 04:03:53 CDT

 Marc wrote:
> I guess it is feasible to use VMD and SMD to do this type of
> simulations.
> 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?

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:57 CST