Using Measure SASA in NAMD Simulations

From: Ajith Rathnaweera Rajapaksha Mudalige (
Date: Mon Apr 16 2012 - 20:22:28 CDT

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.



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