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

[Maik Goette]

Hi

I'm not to sure about how Berk exactly did that.
But, if I understood that correctly, he let things vanish (which is for 
sure the better method, than letting things appear). If he did that, he 
computed the DEsolvation free energy. This actually is the inverse of 
the solvation free energy. Therefore, I think, you have to switch the 
sign of your calculations and you're fine.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Eudes Fileti wrote:
> Hello to 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/
> 
> 
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