Re: Am I doing the Right Thing?

From: Aron Broom (
Date: Thu Jul 12 2012 - 12:36:06 CDT

yes, I think that will work fine. My only point from before is that you
can use:

coordinates NE2_wb.pdb (I'm guessing that is the name of the first
coordinate file you used to begin your simulations)

and keep using that for all subsequent restarts, thereby avoiding having to
do the VMD thing, since the coordinates are only used to get atom names and
such, whereas the actual x,y,z values come from bincoordinates.


On Thu, Jul 12, 2012 at 1:31 PM, Roy Fernando <> wrote:

> 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?
> Roy
> 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

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

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