Hello to 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 clear="all"><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>