Re: Reference file for the constraining force in Umbrella Sampling

From: Chris Harrison (
Date: Sat Mar 14 2009 - 08:19:54 CDT

Mert Gür <> writes:
> Shall I make a ref file from a frame at the end of my constrained simulation
> trajectory to generate the SMDFile file?


> Should my coordinate and structure files at the top of my second SMD
> simulations configuration file be the pdb and psf files I just generate at
> the very beginning of my first SMD simulation and used for my first SMD
> simulation?

Yes. Psf will always be the same. Pdb input to "coordinates" may be the same as long as you are doing a restart (ie bincoordinates) to read in your initial coordinates for the newer run.


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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