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

[Dan Gil]

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!
>> >
>> > 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
>



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