Re: Reference file for the constraining force in Umbrella Sampling

From: Mert Gür (gurmert_at_gmail.com)
Date: Sat Mar 14 2009 - 10:44:31 CDT

Great!
Thanks again for all your help.
Best,
mert

On Sat, Mar 14, 2009 at 3:19 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

>
>
> 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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