[gmx-users] Excluded Volume Effect
samrucu at yahoo.co.in
Tue Jan 24 20:48:15 CET 2017
I want to calculate the excluded volume effect on a protein's dynamics from a protein-in-water trajectory. I used the following command to calculate the volume ----
g_sas -s md.tpr -f md.trr -tv volume.xvg -probe 0
The output file (volume.xvg) has 3 columns - 1st column is time, 2nd column is volume, and 3rd column is density. Does the volume calculated by the above program using probe radius of zero signify the excluded volume? If not, is there any other way by which excluded volume can be calculated?
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