[gmx-users] Re: Free energy - Hydrogen bond solute-solvent - Ethanol as an example.

[Eudes Fileti]

    Hello all
    I have tried to reproduce the hydration free energy (TI) of the ethanol
from Hess and van der Vegt (JPCB, 110, 17616).
    The value I have obtained is around 20kJ/mol while the reference value
is -20.1kJ/mol (if not the sign ...).
    If someone can help me find the mistake I would be very grateful.
    Below are the simulation details.

    I followed the protocol of the paper, Berk:
    I used 47 lambda values (because of hydrogen bonds between
solute-solvent) (dense near lambda=0 and between 0.46 and 0.72).
    I am turning off the LJ and Coulomb terms separately.
    Softcore (alpha = 0.5, power = 1), OPLS-AA
    Timestep = 2fs,
    sd = integrator,
    PME
    constrained = none
    trajectories = 40ps (NVT) (I know that is small, but I looking for
qualitative results) after 20ps of equilibration (NPT).

    I have found a value of -4.8kJ/mol for the DeltaG(vacuum) (relative to
mutate the ethanol to dummy in vacuum).
    My dv/dl curve (for DeltaG(water) is below. Should I expect this form?
    I think there are many "high" positive values. The numerical integration
is 15.9kJ.
    So, DG(hyd) = DG(wat) - DG(vac) = 15.9 - (-4.8) = 20.7kJ

    I believe that this protocol is OK (but I want to confirm that).

    @    title "dG/d\8l\4"
    @    xaxis  label "Time (ps)"
    @    yaxis  label "dG/d\8l\4 (kJ mol\S-1\N [\8l\4]\S-1\N)"
    @TYPE xy
    0.000   4.431073e+02
    0.005   3.660083e+02
    0.010   2.987275e+02
    0.015   2.023206e+02
    0.000   4.431073e+02
    0.005   3.660083e+02
    0.010   2.987275e+02
    0.015   2.023206e+02
    0.020   1.905198e+02
    0.030   1.086573e+02
    0.040   4.217960e+01
    0.050   4.101856e+01
    0.060   2.314358e+01
    0.070   2.223774e+01
    0.080   2.669019e+01
    0.090   1.696131e+01
    0.100   6.089735e+00
    0.110   9.569030e+00
    0.120   1.505562e+01
    0.130   2.785974e+00
    0.140   2.440906e+00
    0.150   3.050463e+00
    0.160   8.578429e-01
    0.200   3.577259e+00
    0.240  -3.532969e+00
    0.280   5.842623e+00
    0.320   7.912565e+00
    0.360   9.322502e+00
    0.400  -2.930754e+00
    0.440   2.797944e+00
    0.460   5.113900e+00
    0.480  -3.919665e+00
    0.500  -9.000282e+00
    0.520  -7.636168e+00
    0.540  -7.574299e+00
    0.560  -2.144124e+01
    0.580  -6.618514e+00
    0.600  -2.755925e+01
    0.620  -1.491331e+01
    0.640  -2.541398e+01
    0.660  -5.213154e+01
    0.680  -2.364612e+01
    0.700  -2.535817e+01
    0.720  -7.767502e+00
    0.760  -1.096362e+01
    0.800   1.136031e+01
    0.840   2.883933e+01
    0.880   4.465743e+01
    0.920   5.461566e+01
    0.960   6.882000e+01
    1.000   7.673736e+01

    --
    _______________________________________
    Eudes Eterno Fileti
    Centro de Ciência Naturais e Humanas
    Universidade Federal do ABC
    Rua Catequese, 242 - 3º Andar
    09090-400 Santo André - SP Brasil
    Tel: +55 11 4437-1600 ramal 408
    skype: eefileti
    http://cromo.ufabc.edu.br/~fileti/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080505/f3802c7b/attachment.html>