Hi gmx-users, I almost reproduced free energy calculations of methane in water on Justin's website. First of all, I am able to follow the workflow of computing solvation free energy for several times with Gromacs version 4.5.7 and version 4.6.2 installed in two identical Linux boxes.
However. the output results of GMX ver 4.5.7 and ver 4.6.2 show different values of dG ################################## GMX Ver. 4.5.7: lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.01 +/- 0.00 lambda 0.100 - 0.150, DG -0.03 +/- 0.01 lambda 0.150 - 0.200, DG -0.08 +/- 0.00 lambda 0.200 - 0.250, DG -0.15 +/- 0.00 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.28 +/- 0.00 lambda 0.350 - 0.400, DG -0.38 +/- 0.00 lambda 0.400 - 0.450, DG -0.50 +/- 0.01 lambda 0.450 - 0.500, DG -0.66 +/- 0.01 lambda 0.500 - 0.550, DG -0.90 +/- 0.01 lambda 0.550 - 0.600, DG -1.21 +/- 0.01 lambda 0.600 - 0.650, DG -1.37 +/- 0.01 lambda 0.650 - 0.700, DG -1.25 +/- 0.01 lambda 0.700 - 0.750, DG -0.96 +/- 0.00 lambda 0.750 - 0.800, DG -0.62 +/- 0.00 lambda 0.800 - 0.850, DG -0.31 +/- 0.00 lambda 0.850 - 0.900, DG -0.03 +/- 0.00 lambda 0.900 - 0.950, DG 0.20 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.31 +/- 0.04 ################################## GMX ver. 4.6.2 ver point 0.000 - 0.050, DG 0.00 +/- 0.00 point 0.050 - 0.100, DG -0.03 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.14 +/- 0.00 point 0.200 - 0.250, DG -0.20 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.34 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.54 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.01 point 0.550 - 0.600, DG -1.24 +/- 0.02 point 0.600 - 0.650, DG -1.39 +/- 0.02 point 0.650 - 0.700, DG -1.28 +/- 0.01 point 0.700 - 0.750, DG -1.00 +/- 0.00 point 0.750 - 0.800, DG -0.67 +/- 0.00 point 0.800 - 0.850, DG -0.36 +/- 0.00 point 0.850 - 0.900, DG -0.09 +/- 0.00 point 0.900 - 0.950, DG 0.14 +/- 0.00 point 0.950 - 1.000, DG 0.33 +/- 0.00 total 0.000 - 1.000, DG -9.23 +/- 0.03 ################################## The value of DG (= -9.23 kJ mol -1) by GMX ver 4.6.2 is very close to that by Justin or Shirts et.al of 2.24 kcal mol-1 (~ -9.36 kJ mol -1), while that of GMX ver 4.5.7 ( =-8.31 kJ mol-1) is far away. I wonder if someone has similar experience to explain the inconsistency between the outputs from ver 4.5.7 (~-8.31 kJmol-1) and ver 4.6.2 (-9.23 kJmol-1 ), despite the values of dG computed by others. Second, the reason why I almost reproduced dG but not completely is because I removed the step of L- BFGS minimization. I was not able to pass this step for both GMX versions. Here shows the warning. ++++++++++++++++++++++++++++ Fatal error: The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent). ++++++++++++++++++++++++++++ L-BFGS mdp file can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_l-bfgs.mdp Again, I appreciate advice or a hint. Thanks, Dwey -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists