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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hello gmx-users<br>
<br>
I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like<br>
<br>
g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg <br>
<br>
This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane. I think this has to do with the fact that the surface calculation
method used in g_sas is missing the void in the centre of the ring. In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane. I found that in this case the volume of the cyclic molecule was expectedly smaller.
I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes.<br>
<br>
Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems. Also I am wondering if anybody can suggest any other free software that
would allow me to compute van der Waal's and Solvent Excluded volumes.<br>
<br>
Thanks in advance.<br>
<br>
Jake Spooner<br>
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