Re: Simulation Using Both NAMD and VMD

From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Apr 20 2012 - 17:30:14 CDT

Is it possible to use the tcl forces capability of NAMD to run the script
you want? As Axel points out, passing the information into VMD at every
timestep would be crippling (unless your simulation takes an extremely long
time per timestep already). If you only need to update the forces every
1000 timesteps or something, that might work.

~Aron

On Fri, Apr 20, 2012 at 6:10 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Apr 20, 2012 at 6:05 PM, Ajith Rathnaweera Rajapaksha Mudalige
> <arajapak_at_purdue.edu> wrote:
> > Hi Everybody,
> >
> > Is it possible to write a script for a NAMD simulation to access VMD at
> each time step through Interactive Molecular Dynamics mode (or any other
> possible way).
>
> technically yes. in practice no, since that would be highly inefficient.
> better to implement what you need into NAMD directly.
>
> axel.
>
> > In my simulation I need to execute some VMD commands at each time step
> and define a new force according to the results output from VMD.
> >
> > I highly appreciate if someone could shed some light in this direction.
>
>
>
>
> > Regards,
> >
> > Ajith
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>

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

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