Re: Am I doing the Right Thing?

From: Aron Broom (
Date: Thu Jul 12 2012 - 12:10:43 CDT

are you using binary inputs? If not, then you should just be using the
restart coordinate file as your input for the next window. If you are
using binary coordinates, then you are supplying the coordinates from the
restart as "bincoordinates", and for "coordinates" you are just suppling
the pdb you used for the first window, as the actual coordinates in it
don't matter. You can also do what you are doing, it will work fine
(assuming we are talking about binary coordinates here), but it's not
necessary to do that re-writing every time.

On Thu, Jul 12, 2012 at 1:02 PM, Roy Fernando <> wrote:

> 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
> Roy

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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