Re: Simulation Using Both NAMD and VMD

From: Ajith Rathnaweera Rajapaksha Mudalige (
Date: Fri Apr 20 2012 - 18:14:17 CDT


Thanks Alex, Aron,

Yes, practically I will want to update the forces after every 500 time steps or so.

I know this will slow down the simulation but it is an essential step to run the simulation correctly.

The forces I am applying to my system is depending on Solvent Accessible Surface (SAS) of the molecule. SAS can be determined using "measure SASA" command in VMD. This is not directly supported in NAMD (please correct me if I am wrong). Therefore, I need to run the simulation in NAMD load the current phase in VMD and determine SAS at that point, determine the direction of the forces, get back to NAMD and run for the next phase.

Is this possible?

I will highly appreciate if anyone can give me a little concrete example, if anyone has done this type of a work before.



----- Original Message -----
From: "Aron Broom" <>
To: "Axel Kohlmeyer" <>
Cc: "Ajith Rathnaweera Rajapaksha Mudalige" <>,
Sent: Friday, April 20, 2012 6:30:14 PM
Subject: Re: namd-l: Simulation Using Both NAMD and VMD

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.


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

On Fri, Apr 20, 2012 at 6:05 PM, Ajith Rathnaweera Rajapaksha Mudalige
< > 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.


> 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 
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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