[gmx-users] Calculating hydrogen bonding density - issues with g_sas?
Teemu Murtola
teemu.murtola at gmail.com
Sun Jul 19 17:22:33 CEST 2015
Hi,
and sorry for a bit late reply. g_sas (or gmx sasa) does not compute the
volume correctly if your solute crosses a periodic boundary. In 5.1, there
is a note to this effect in the documentation, but it is tricky to actually
detect this condition in the code. But what this means is that you cannot
compute the volume of, e.g., a periodic slab using g_sas. With proper use
of trjconv, you can still compute the volume of a multi-molecule droplet.
Best regards,
Teemu
On Wed, Jul 8, 2015 at 6:59 PM Dan Gil <dan.gil9973 at gmail.com> wrote:
> Is g_sas applicable to more than one molecule at a time?
>
> I have 4500 water molecules in the liquid state. I am using the command:
> g_sas -f traj.trr -s topol.tpr -tv volume.xvg
>
>
> On Tue, Jul 7, 2015 at 10:31 AM, Dan Gil <dan.gil9973 at gmail.com> wrote:
>
> > 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!
>
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