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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