From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Tue Jun 21 2005 - 18:56:45 CDT
you could use this three lines in your .conf or .namd
# FIXED ATOMS
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
changes.
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
Leonardo
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