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

[Mark Abraham]

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.

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

See the manual first.

>    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?

Mark