[gmx-users] 'hydration energy'

[Markus O Kaukonen]

Hei Kaikki,

Experimentally hydration energy of H3O+ molecule
(that is energy gain when taking H3O+ from vacuum to water) is of the
order of 1000kJ/mol.

Now, I did a gromacs run with a protein in water with periodic bondary
conditions and got 'hydration energy' (that is here the
energy difference) between BH+ and B
B:   protein in water with a base non-protoned
BH+: protein in water with a base protonated
The difference between B and BH+ being thus one proton.

I get Energy(BH+) - Energy(B) = -6000 kJ/mol
which is obviously too big a number.

I guess that this is because of too small cutoff's (see below),
perhaps in (BH+) waters come closer to protein and start to interact???
The final srtuctures (BH+) and (B) look similar.

Or is there some other explanation (like mistake made below)?

Terveisin, Markus



;
;	User mokaukon
;	Wed Nov  3 17:12:44 1993
;	Input file
;
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
integrator          =  cg
nsteps              =  2000
;dt                  =  0.001



; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 10
nstvout                  = 10000
nstfout                  = 10000

; Output frequency for energies to log file and energy file
nstlog                   = 1
nstenergy                = 1

comm-mode                = None

pbc                      = xyz

ns_type                  = grid

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rlist = 1.10
rcoulomb = 1.00
rcoulomb_switch = 0.0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r                = 1.00
; Method for doing Van der Waals
vdw-type                 = shift
; cut-off lengths
rvdw-switch              = 0.80
rvdw                     = 0.90
; Apply long range dispersi0n corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.075

; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no


;	Energy minimizing stuff
;
emtol               =  10
emstep              =  0.01
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10



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