Hello all<br> I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616).<br> The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...).<br>
If someone can help me find the mistake I would be very grateful.<br> Below are the simulation details.<br><br> I followed the protocol of the paper, Berk:<br> I used 47 lambda values (because of hydrogen bonds between solute-solvent) (dense near lambda=0 and between 0.46 and 0.72).<br>
I am turning off the LJ and Coulomb terms separately.<br> Softcore (alpha = 0.5, power = 1), OPLS-AA<br> Timestep = 2fs,<br> sd = integrator,<br> PME<br> constrained = none<br> trajectories = 40ps (NVT) (I know that is small, but I looking for qualitative results) after 20ps of equilibration (NPT).<br>
<br> I have found a value of -4.8kJ/mol for the DeltaG(vacuum) (relative to mutate the ethanol to dummy in vacuum).<br> My dv/dl curve (for DeltaG(water) is below. Should I expect this form?<br> I think there are many "high" positive values. The numerical integration is 15.9kJ.<br>
So, DG(hyd) = DG(wat) - DG(vac) = 15.9 - (-4.8) = 20.7kJ<br><br> I believe that this protocol is OK (but I want to confirm that).<br><br> @ title "dG/d\8l\4"<br> @ xaxis label "Time (ps)"<br>
@ yaxis label "dG/d\8l\4 (kJ mol\S-1\N [\8l\4]\S-1\N)"<br> @TYPE xy<br> 0.000 4.431073e+02<br> 0.005 3.660083e+02<br> 0.010 2.987275e+02<br> 0.015 2.023206e+02<br> 0.000 4.431073e+02<br>
0.005 3.660083e+02<br> 0.010 2.987275e+02<br> 0.015 2.023206e+02<br> 0.020 1.905198e+02<br> 0.030 1.086573e+02<br> 0.040 4.217960e+01<br> 0.050 4.101856e+01<br> 0.060 2.314358e+01<br>
0.070 2.223774e+01<br> 0.080 2.669019e+01<br> 0.090 1.696131e+01<br> 0.100 6.089735e+00<br> 0.110 9.569030e+00<br> 0.120 1.505562e+01<br> 0.130 2.785974e+00<br> 0.140 2.440906e+00<br>
0.150 3.050463e+00<br> 0.160 8.578429e-01<br> 0.200 3.577259e+00<br> 0.240 -3.532969e+00<br> 0.280 5.842623e+00<br> 0.320 7.912565e+00<br> 0.360 9.322502e+00<br> 0.400 -2.930754e+00<br>
0.440 2.797944e+00<br> 0.460 5.113900e+00<br> 0.480 -3.919665e+00<br> 0.500 -9.000282e+00<br> 0.520 -7.636168e+00<br> 0.540 -7.574299e+00<br> 0.560 -2.144124e+01<br> 0.580 -6.618514e+00<br>
0.600 -2.755925e+01<br> 0.620 -1.491331e+01<br> 0.640 -2.541398e+01<br> 0.660 -5.213154e+01<br> 0.680 -2.364612e+01<br> 0.700 -2.535817e+01<br> 0.720 -7.767502e+00<br> 0.760 -1.096362e+01<br>
0.800 1.136031e+01<br> 0.840 2.883933e+01<br> 0.880 4.465743e+01<br> 0.920 5.461566e+01<br> 0.960 6.882000e+01<br> 1.000 7.673736e+01<br><br> -- <br> _______________________________________<br>
Eudes Eterno Fileti<br> Centro de Ciência Naturais e Humanas<br> Universidade Federal do ABC<br> Rua Catequese, 242 - 3º Andar<br> 09090-400 Santo André - SP Brasil<br> Tel: +55 11 4437-1600 ramal 408<br>
skype: eefileti<br> <a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a> <br><br><br><br>