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

[Dan Gil]

I am using the default radius of 0.14 nm. In this case, I believe that it
is consistent. Nevertheless, I have tried using a probe much larger with no
significant difference in the results.
The way I am using g_sas is: I have 4500 water molecules. I specified that
I want the volume of all of them.

On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

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