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
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