Re: Fixed restraint

From: Leonardo Sepulveda Durán (
Date: Tue Jun 21 2005 - 18:56:45 CDT

you could use this three lines in your .conf or .namd

fixedAtoms on
fixedAtomsForces on
fixedAtomsCol O; # If Ocupancy column=0.00 then that atom isn't fixed

and put 0.00 in the ocupancy column of the atoms you want to mantain
fixed in your imput pdb file, and change all others to 1.00. That will
mantain the coordinates of that atoms unchanged while all around

you could minimize then, and run a molecular dynamics without the
fixed atom with

minimize 1000 # fixed
fixedAtoms off # turn off fixed atoms
run 2000 # unfixed atoms

but you cannot turn fixedAtoms on again from that scrript


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:52 CST