From: mdcooper (mdcooper_at_uvic.ca)
Date: Fri Sep 24 2004 - 14:32:46 CDT
Just a question about SMD.
I am running a script that minimizes for a while then run smd on a ligand and
then minimizes ...
each time I repeat I recall the smd config file, which means that SMDFile is
picked again. What I want to know is:
does SMDFile actually specify the atom positions as well as the atoms that
should be affected by the SMD, or are the atom position specified by the
coordinate file read in initially and SMDFile is just a reference for the SMD
I ask because i only want to make the SMDfile once and not have to update it
after every minimization.
SMDFile SMD constraint reference position
Acceptable Values: UNIX filename
Description: File to use for the initial reference position for the SMD
harmonic constraints. All atoms in this PDB file with a nonzero value in the
occupancy column will be tagged as SMD atoms. The coordinates of the tagged
SMD atoms will be used to calculate the initial center of mass. During the
simulation, this center of mass will move with velocity SMDVel in the
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