Reference file for the constraining force in Umbrella Sampling

From: Mert Gür (
Date: Thu Mar 12 2009 - 18:02:24 CDT

 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

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 {

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