From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sat Mar 14 2009 - 08:19:54 CDT
Mert Gür <gurmert_at_gmail.com> writes:
> Shall I make a ref file from a frame at the end of my constrained simulation
> trajectory to generate the SMDFile file?
Yes
>
> 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.
C.
-- 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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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