From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 03 2006 - 02:08:09 CST
Restrain one part of the protein harmonically (
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html ) and apply SMD to
the other (constant force or constant velocity -
You need to use VMD to create two pdb files used for these. For harmonic
constraints, the file given for "consref" contains the positions, the file
for "conskfile" contains the force constants. Often, they can be the same.
So in VMD, you could make an atomselection for the atoms to be restrained
and then use this:
$sel set occupancy 5
to give them a force constant (5 is just an example). Before doing this
though, be sure to set all the atoms' occupancy to 0 (just use "atomselect
top all"). Once done, make a selection for all the atoms and write a pdb.
This will be the restrained atoms.
For constant velocity SMD, the occupancy column only tells if the atoms
should be pulled or not; the direction, velocity, and force constant are
specified in the configuration. Again, simply use VMD to make a selection
for those atoms, set their occupancy to 1, and then write another pdb for
the whole system (REMEMBER: set all the occupancies to 0 again before doing
For constant force pulling, you will need a pdb file that specifies the
direction and forces. Here, the x,y,z columns specify the direction and O
the scaling factor for the force. Again, you set O to zero for all the
atoms, and then set it to 1 (or some other scaling factor depending on what
force you want - units are given in the NAMD Manual linked above) for the
atoms you wish to apply force to. Their x, y, and z components of force can
be set in the same way as above (i.e. "$sel set x 0").
Hopefully this fills in the gaps in the User's Guide for you well enough.
Let us know if you get stuck again.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Al-Rawi, Ahlam
Sent: Thursday, November 02, 2006 12:16 PM
Subject: namd-l: external force
Could I get your help please.
I have a system that contain B-sheet formed by two proteins in solution.
I need to apply external force to pull away the two proteins that form the
I read the on-line document, but I am not sure that I understand what kind
of changes I need to do and where in the pdb file and the configuration
Kansas State University
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