VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 16 2012 - 23:39:24 CDT

Hi,
  To my knowledge, NAMD doesn't have a SASA measurement feature built-in,
so you would compute this by post-processing the trajectory files your
simulation produces with VMD or a similar tool.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 16, 2012 at 07:54:32PM -0400, Ajith Rathnaweera Rajapaksha Mudalige wrote:
> Hi,
>
> I am Ajith a Physics Graduate Student at Purdue University.
>
> I am working on a simulation where at each time step I need to apply a force on every surface atom, in a direction perpendicular to the solvent accessible surface.
>
> I noticed, the features of "measure sasa" is providing all the details I want, but can I use "measure sasa" in NAMD simulations?
>
> I highly appreciate your input in this matter. Please let me know what choices I have in here.
>
> Regards,
>
> Ajith 

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