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

[Mark Abraham]

Hi,

Is the radius being used consistent with your assumption?

Mark

On Tue, Jul 7, 2015 at 3:58 PM Dan Gil <dan.gil9973 at gmail.com> wrote:

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