Re: Am I doing the Right Thing?

From: Roy Fernando (
Date: Thu Jul 12 2012 - 12:31:36 CDT

Hi Aron,

Thanks for the message. Yes I am using binary inputs.
For example my restart configuration file will look like the following.

structure NE2_wb.psf
coordinates NE2_wb_eq1.pdb
bincoordinates NE2_eq1_data.restart.coor
binvelocities NE2_eq1_data.restart.vel
extendedSystem NE2_eq1_data.restart.xsc

So I am fine, is that what you say?


On Thu, Jul 12, 2012 at 1:10 PM, Aron Broom <> wrote:

> 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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