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

[Frankie Montenegro]

On 9/11/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Frankie Montenegro wrote:
> > Hi again guys,
> >
> > Few more questions:
> >
> > 1. I would like to calculate compressibility of the protein+water
> > system, but separating it into bulk water, hydration water and
> > protein.  So I need to pick these and compute volumes separately. When
> > picking hydration water molecules, two tools are mentioned on the
> > List: trjorder and g_hbond. Which one would you recommend for my task?
>
> Don't know, but I'd start by reading the man pages for each of those tools.
>

I did that. They both seem OK to me. I am not that experienced with
Gromacs though, which is why I'm asking for suggestion.

> > 2. a)The program g_energy gives output for compressibility. What
> > method was used for that calculation?
>
> See the manual first.
>


Did that too. Didn't find anything. I suppose I could go through the code.


> >    b) When running g_energy I noticed a particularly crappy number for
> > the specific heat of SPC water with ffgmx forcefield. It is about
> > 17J/mol.K (should be about 75).
> > I get similar number with my code using energy fluctuation method.
> > Do you guys have any suggestions? I cut and paste my equilibration and
> > production run mdp files.
>
> Why are you generating velocities post-equilibration?
>

Upps! Thanks.