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

[Frankie Montenegro]

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?

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).
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