Running Multiple TMD simultaneously

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sat Sep 27 2008 - 14:57:09 CDT

I was wondering if there was a straightforward way to rig namd to run
two TMD simulations simultaneously? I want to drive two different
domains into different conformations, but I don't want them to be
correlated in any way. In other words, I want to drive the two domains
to particular conformations, but I don't want the fitting of the two
to be done together or relative to one another.

The simplest way to do this would be to just do TMD in two steps. You
could drive one domain to the desired conformation, and then drive the
other domain holding the first one restrained to the target position.
This would be sub-optimal since it would take twice as much simulation
time.

My previous experiences writing GlobalMaster-based source hacks of
namd is that you can't run two different GlobalMaster processes at the
same time, so I don't think I can just go in and duplicate the TMD
code and just call it something like TMD2 and then call them both in
the config file.

Any suggestions would be most appreciated.

Josh

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