[gmx-users] 'hydration energy'

[david.evans at ulsop.ac.uk]

Hi,

Could you spell out exactly how you calculated the -6000 kJ/mol
figure?
The extra proton will interact with the rest of the protein, as well
as with the water, but this doesn't contribute 
directly to the hydration energy, because this interaction is also
present in the (hypothetical) unhydrated protein.
It may be that you've taken this  into account, but it's not clear
from your message.

Dave

--

Dr David Evans
London School of Pharmacy


---- Message from Markus O Kaukonen <mokaukon at cc.helsinki.fi> at
2004-10-14 12:22:26 ------
>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
>
>
>
>-- 
>-----------www= http://www.iki.fi/markus.kaukonen---------------
>Markus.Kaukonen at helsinki.fi   \ HOME->   Verajakallionkatu 6 a 5
>Helsinki Bioenergetics Group   \_______  02600 Espoo, Finland
>Institute of Biotechnology             \ tel:+358-(0)9-5127122/h
>Biocenter 3, P.O.BOX 65 (Viikinkaari 1) \____
>FIN-00014 University of Helsinki              \______ H+ ______
>tel: +358-(0)9-19159752/o, fax: +358-(0)9-19159920             \
>--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---
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