Re: targeted molecular dynamics

From: Chris Harrison (
Date: Thu Oct 14 2010 - 17:28:22 CDT

TMDFile = target structure
TMD is active during MD. It is not a minimization method. You could
perhaps try cooling your system to 0 and perform a TMD MD. That might
be as close to a "TMD minimization" as you would get. But this is not
the intended purpose for the method, so "buyer beware."


On Thu, Oct 14, 2010 at 5:22 PM, <> wrote:
> Hi,
> I try to write a script in order to do targeted molecular dynamics, but I do not
> understand some things:
> the TMDFile must be the initial pdb or the pdb that refers to the target
> structure(final structure)?
> Also, this segment will be part of a minimization script, how can I run it?
> Thank you in advance.

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078

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