Re: Running Multiple TMD simultaneously

From: Axel Kohlmeyer (
Date: Sun Sep 28 2008 - 13:24:16 CDT

On Sat, 27 Sep 2008, Joshua Adelman wrote:

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


if you drive both domains at the same time, you are correlating
them by construction and thus i don't think it would make much
of a difference to consider them as just one domain. the big
question is: are you actually interested in the transition path?
or do just want to drive the system from one config to the other?
if it is the first case, then i don't think you have much of a
choice other than looking at each of them independently. perhaps
some other method than TMD (metadynamics or ABF) that allows to
describe the transition(s) with independent collective variables
might be an alternative. of course there is also always the
possibility, that the two transitions are actually correlated
in some way...


JA> The simplest way to do this would be to just do TMD in two steps. You could
JA> drive one domain to the desired conformation, and then drive the other
JA> domain holding the first one restrained to the target position. This would
JA> be sub-optimal since it would take twice as much simulation time.
JA> My previous experiences writing GlobalMaster-based source hacks of namd is
JA> that you can't run two different GlobalMaster processes at the same time, so
JA> I don't think I can just go in and duplicate the TMD code and just call it
JA> something like TMD2 and then call them both in the config file.
JA> Any suggestions would be most appreciated.
JA> Josh

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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