[gmx-users] Calculating hydrogen bonding density - issues with g_sas?

Dan Gil dan.gil9973 at gmail.com
Tue Jul 7 15:58:05 CEST 2015


I am using g_hbond to count the number of h-bonds and then g_sas to
calculate the volume. I want to get the number of hydrogen bonds per
volume. But I am having issues with g_sas - the volume calculated is about
one half of the expected value. For instance, in a pure water system (NVT,
SPCE, T=300K) periodic in the x and y directions, volume was found to be
about 60nm^3, whereas I expected 130nm^3.

I would appreciate any advice!


Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
dan.gil9973 at gmail.com

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