Constraints in NAMD

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Wed Apr 22 2009 - 09:50:37 CDT

Hello,
I want to apply harmonic constraints to some atoms of my system.
To my understanding I have to set

constraints on
consexp 2
consref <PDB FILE WITH REFERENCE COORDINATES>
conskfile <FILE WITH FORCE CONSTANTS>
conskcol <COLUMN ID TO GRAB TO FORCE CONSTANTS FROM>
..

I dont get several things:

1/ I want to make en energy minimization and then apply restraints.
Does that mean that I can not do this in a single run - first I have
to do the EM, then acquire resulting pdb file and only then start a
new simulation specifying this file as the reference one?
2/ What is the format of consref and conskfile files? I could not find
any examples of the files on the web - only the config file options.
Can you show me yours?
3/ I want to gradually decrease the restraints on my atoms. Could I do
this in a single run?
4/ What value is the general maximum for force constraint in NAMD? I
mean, for example in gromacs setting posres constant to more than 1000
kJ/mol nm is generally useless since nothing moves already at this
value.

Thank you for your time and patience.
SDA

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