[gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

[Frankie Montenegro]

On 9/11/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Frankie Montenegro wrote:

> That sounds difficult because computing volume is difficult. We should
> write a better program for this, but the problem lies in definition:
> where does one water molecule stop and the next begin?
>
> >

Thanks. I was hoping to use Voronoi volume for compressibility
calculation. That should ensure that individual partial volumes add up
to the complete volume. So, is any of the two (trjorder vs g_hbond)
better?

> This is because of Berendsen coupling. It should be better with
> Nose-Hoover or without (using shifted vdw potential as well).

I suspected Berendsen coupling might be the problem. Should I expect
anything close to the measured value with Nose-Hoover, but keeping vdw
the way it is?

Regards,
Frankie