VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Apr 16 2019 - 12:17:26 CDT

The SASA calculation in "measure sasa" is pretty straightforward, and doesn't consider periodic boundaries at all. Instead it samples N points (where by default N=500) around each atom in the selection, and asks if they are solvent accessible or not. This fraction multiplied by the surface area of the sphere with radius atom radius + probe radius is where the SASA comes from. So making sure your compound isn't split across a periodic boundary is important, but measure sasa doesn't care about the PBC dimensions otherwise.

-Josh

On 2019-04-16 04:59:07-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
Hello,

I am trying to calculate SASA of a part of system from a lammps trajectory file in vmd. My system is already wrapped in a box and box-length is given in the trajectory file. I just wanted to know if VMD automatically include periodic images during SASA calculation or I have to provide it. Thanks.

Best,
Projesh Kumar Roy

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