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

[David van der Spoel]

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?
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?

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

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

> 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.
> 
> ----------------------------
> Equilibration
> ----------------------------
> Thanks,
> Frankie
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> tinit               =  0.0
> dt                  =  0.001    ; ps !
> nsteps              =  10000    ; total 10 ps.
> nstcomm             =  1
> nstxout             =  1000
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  10
> ns_type             =  grid
> 
> comm-mode           =  Angular
> nstcomm             =  1
> comm-grps           =  System
> 
> pbc                 =  xyz
> 
> coulombtype         =  PME
> rvdw                =  0.9
> rlist               =  0.9
> rcoulomb            =  0.9
> fourierspacing      =  0.12
> pme_order           =  4
> ewald_rtol          =  1e-5
> 
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             = System
> tau_t               =  0.1
> ref_t               =  275
> ; Energy monitoring
> energygrps          = System
> ; Pressure coupling is not on
> Pcoupl              =  no
> ; Random seed for Andersen thermostat
> andersen_seed            = 815131
> ; Generate velocites is on at 275 K.
> gen_vel             =  yes
> gen_temp            =  275.0
> gen_seed            =  173529
> 
> ------------
> NVT run
> ------------
> cpp                 =  /lib/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  1100000  ; total 1.1ns.
> nstcomm             =  1
> nstxout             =  1000
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  1000
> nstenergy           =  1000
> nstlist             =  10
> ns_type             =  grid
> 
> comm-mode           =  Angular
> nstcomm             =  1
> comm-grps           =  System
> 
> pbc                 =  xyz
> 
> coulombtype         =  PME
> rvdw                =  0.9
> rlist               =  0.9
> rcoulomb            =  0.9
> fourierspacing      =  0.12
> pme_order           =  4
> ewald_rtol          =  1e-5
> 
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =  System
> tau_t               =  0.1
> ref_t               =  275
> ; Energy monitoring
> energygrps          =  System
> ; Pressure coupling is not on
> Pcoupl              =  no
> ; Generate velocites is on at 275 K.
> gen_vel             =  yes
> gen_temp            =  275.0
> gen_seed            =  173529
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se