Re: Simulation Using Both NAMD and VMD

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 20 2012 - 19:04:54 CDT

On Fri, Apr 20, 2012 at 7:14 PM, Ajith Rathnaweera Rajapaksha Mudalige
<arajapak_at_purdue.edu> wrote:
> Hi
>
> 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?

sure, but how many times do i need to repeat it?
just implement a SASA measurement into NAMD.
that would be *far* less work than everything else.

what you propose to do is insanity.

axel.

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

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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