Re: Reference file for the constraining force in Umbrella Sampling

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Thu Mar 12 2009 - 18:30:07 CDT

No, the restraint file uses the coordinates within that pdb file as
equilibrium positions from which to apply the constraint - you will
have to make a new ref file from a frame at the end of your smd
trajectory once the protein is where you want it to be. You might as
well use this same file for the spring constant file (kfile) putting
the spring constants in the occupancy column.

-Eric

On Mar 12, 2009, at 6:02 PM, Mert Gür wrote:

> Hi everyone,
> What I am trying to is:
> I first move my protein(prot.psf,prot.pdb) along my reaction
> coordinates with steered molecular dynamics. Lets say its stops at a
> final position.
> I want to apply constraining potential at that point. What should I
> take to generate my consref and conskfile files . Should it be the
> same coordinates with
>
> prot.pdb which I used in SMD as coordinates prot.pdb
>
> or should I use the final restartcoordinates of my SMD simulation.
> Or does it even not make any difference which coordinates I use for
> my consref and conskfile files .
>
> if {$cons == 1} {
>
> constraints on
>
> consexp 2
>
> consref $ref_res
>
> conskfile $ref_res
>
> conskcol O
>
> selectConstraints on
>
> selectConstrX off
>
> selectConstrY off
>
> selectConstrZ on
>
> } else {
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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