From: Nicholas Musolino (musolino_at_mit.edu)
Date: Fri Sep 10 2010 - 07:48:46 CDT
So, in an earlier e-mail E. Enriques provided some good ideas about using separate files.
The other possibility is to use VMD in an automated way to do this. The basic approach would be:
1. Run VMD; you can load your PSF and .coor files by providing them as command-line arguments.
2. Create an atom selection for all the atoms you would like to be fixed. You could use a simple selection approach (listing atom indices) or a more elegant one (all atoms with a certain name) if possible.
3. Set beta for selection (see http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html).
4. Write a new PDB file, which will have the appropriate beta values.
All this can be automated a great deal using TCL files, shell scripts, etc., but there's a bit of a learning curve to all that.
Hope this is helpful!
On Sep 10, 2010, at 1:57 AM, Swarna M Patra wrote:
> Hi Namd users
> is it possible to assign a value for beta column for protein or lipid to write in the output file. so that I can take the output pdb file for my constraint file and continue the simulation without stopping. Now after each simulation I take the .coor file convert it to pdb and change the beta for desired atoms. if anyone knows any other alternative method to give restrain in pdb file let me know.
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