Re: Using Measure SASA in NAMD Simulations

From: Aron Broom (
Date: Tue Apr 17 2012 - 02:02:16 CDT

You might want to see if you can look into the Generalized Born portion of
NAMD, there is already code that calculates SASA as part of the GB implicit
solvent calculations. The main reason I'd suggest looking into this rather
than implementing something yourself through tcl, is that an SASA
calculation can be a bit time consuming and would grind your simulation to
a halt, but the method used in the GB stuff is extremely fast.


On Mon, Apr 16, 2012 at 9:22 PM, Ajith Rathnaweera Rajapaksha Mudalige <> wrote:

> Hi All,
> 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 "VMD measure sasa" is providing all the details
> I want, but can I use "measure sasa" in NAMD simulations?
> 1) Using Measure SASA I can obtain the coordinates of the points on the
> surface of the solvent accessible surface. (This surface can be found
> separately for each atom and the atoms with zero surface area are the atoms
> buried inside the molecule)
> 2) These coordinates can be use to found the normal directions to the
> points.
> 3) sum of all the normal directions for a surface atom is the direction I
> want to apply the force
> All this ideas are sensible if only I can use measure SASA inside a tcl
> cript in a NAMD simulation.
> I highly appreciate your input in this matter. Please let me know what
> choices I have in here.
> Regards,
> Ajith

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

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