Am I doing the Right Thing?

From: Roy Fernando (
Date: Thu Jul 12 2012 - 12:02:05 CDT

Hi all,

I have a question to ask, just to verify if I am doing the right thing.
I am doing a TCL force simulation in segments. I need to study short time
scale effects to the structure under the action of the external forces
(Defined in the TCL script).

So I run the simulation, say for 1000 time steps. Then, I need to restart
the simulation with the structure produced at the end of the first part. In
the restart configuration file I can use the restart files generated in the
first part. But I also need a pdb coordinate file.

To generate that coordinate file, I load the restart.coor file on to the
system psf file in VMD and just write a pdb file for that. This pdb file I
am using as the coordinate file in the restart simulation. Is this the
correct methodology?

I appreciate your input


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