Re: [gmx-users] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
On 6/23/13 1:13 AM, Dwey wrote: Hi Justin, Thank you for sharing your experience with me. As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box and I am able to reproduce a similar result ( DG= -9.30 kJmol-1). Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while Gromacs ver 4.5.7 as reported earlier is installed with pre-compiled binary files. Thus, Gromacs ver 4.5.7 is now re-compiled again by myself. Below are shown results. In addition, L-BFGS mdp file works well for all versions after it is modified by adding define = -DFLEXIBLE. Gromacs ver 4.5.5 (compiled from source codes) point 0.050 - 0.100, DG -0.04 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.13 +/- 0.01 point 0.200 - 0.250, DG -0.19 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.35 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.55 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.00 point 0.550 - 0.600, DG -1.25 +/- 0.00 point 0.600 - 0.650, DG -1.40 +/- 0.01 point 0.650 - 0.700, DG -1.29 +/- 0.01 point 0.700 - 0.750, DG -1.01 +/- 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 0.050 - 1.000, DG -9.30 +/- 0.03 Gromacs ver 4.5.7 (compiled from source codes) lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.02 +/- 0.00 lambda 0.100 - 0.150, DG -0.04 +/- 0.00 lambda 0.150 - 0.200, DG -0.09 +/- 0.00 lambda 0.200 - 0.250, DG -0.14 +/- 0.01 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.29 +/- 0.01 lambda 0.350 - 0.400, DG -0.37 +/- 0.00 lambda 0.400 - 0.450, DG -0.48 +/- 0.01 lambda 0.450 - 0.500, DG -0.65 +/- 0.01 lambda 0.500 - 0.550, DG -0.89 +/- 0.01 lambda 0.550 - 0.600, DG -1.19 +/- 0.01 lambda 0.600 - 0.650, DG -1.34 +/- 0.01 lambda 0.650 - 0.700, DG -1.23 +/- 0.00 lambda 0.700 - 0.750, DG -0.95 +/- 0.01 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 0.19 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.19 +/- 0.03 After comparing the output from ver 4.5.5 with that from ver 4.5.7, I do find quirky information from the g_bar in ver 4.5.7. In ver 4.5.7, for example, it shows that ver 4.5.7 dose not give information of dH/dl (see below) Moreover, I also try g_bar of ver 4.5.5 or 4.6.2 to process the output data (such as md*.xvg generated by ver 4.5.7). The result is unchanged and DG ( -8.19 kJmol-1) remains incorrect. Thanks, Dwey ++ g_bar ver 4.5.7, md0.05.xvg: 0.0 - 5000.0; lambda = 0.050 foreign lambdas: 0.050 (250001 pts) 0.000 (250001 pts) 0.100 (250001 pts) md0.15.xvg: 0.0 - 5000.0; lambda = 0.150 foreign lambdas: 0.150 (250001 pts) 0.100 (250001 pts) 0.200 (250001 pts) md0.1.xvg: 0.0 - 5000.0; lambda = 0.100 foreign lambdas: 0.100 (250001 pts) 0.050 (250001 pts) 0.150 (250001 pts) . . . g_bar ver 4.5.5 or 4.6.2, md0.05.xvg: 0.0 - 5000.0; lambda = 0.05 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0 (250001 pts) delta H to 0.1 (250001 pts) md0.15.xvg: 0.0 - 5000.0; lambda = 0.15 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0.1 (250001 pts) delta H to 0.2 (250001 pts) md0.1.xvg: 0.0 - 5000.0; lambda = 0.1 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0.05 (250001 pts) delta H to 0.15 (250001 pts) . . . Thanks for the detailed information. Please file a bug report on redmine.gromacs.org with all of this information. We had intended for 4.5.7 to be the final version in the 4.5.x series, but if there are serious issues with it, they should probably be corrected. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
Hi Justin, Thank you for sharing your experience with me. As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box and I am able to reproduce a similar result ( DG= -9.30 kJmol-1). Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while Gromacs ver 4.5.7 as reported earlier is installed with pre-compiled binary files. Thus, Gromacs ver 4.5.7 is now re-compiled again by myself. Below are shown results. In addition, L-BFGS mdp file works well for all versions after it is modified by adding define = -DFLEXIBLE. Gromacs ver 4.5.5 (compiled from source codes) point 0.050 - 0.100, DG -0.04 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.13 +/- 0.01 point 0.200 - 0.250, DG -0.19 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.35 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.55 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.00 point 0.550 - 0.600, DG -1.25 +/- 0.00 point 0.600 - 0.650, DG -1.40 +/- 0.01 point 0.650 - 0.700, DG -1.29 +/- 0.01 point 0.700 - 0.750, DG -1.01 +/- 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 0.050 - 1.000, DG -9.30 +/- 0.03 Gromacs ver 4.5.7 (compiled from source codes) lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.02 +/- 0.00 lambda 0.100 - 0.150, DG -0.04 +/- 0.00 lambda 0.150 - 0.200, DG -0.09 +/- 0.00 lambda 0.200 - 0.250, DG -0.14 +/- 0.01 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.29 +/- 0.01 lambda 0.350 - 0.400, DG -0.37 +/- 0.00 lambda 0.400 - 0.450, DG -0.48 +/- 0.01 lambda 0.450 - 0.500, DG -0.65 +/- 0.01 lambda 0.500 - 0.550, DG -0.89 +/- 0.01 lambda 0.550 - 0.600, DG -1.19 +/- 0.01 lambda 0.600 - 0.650, DG -1.34 +/- 0.01 lambda 0.650 - 0.700, DG -1.23 +/- 0.00 lambda 0.700 - 0.750, DG -0.95 +/- 0.01 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 0.19 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.19 +/- 0.03 After comparing the output from ver 4.5.5 with that from ver 4.5.7, I do find quirky information from the g_bar in ver 4.5.7. In ver 4.5.7, for example, it shows that ver 4.5.7 dose not give information of dH/dl (see below) Moreover, I also try g_bar of ver 4.5.5 or 4.6.2 to process the output data (such as md*.xvg generated by ver 4.5.7). The result is unchanged and DG ( -8.19 kJmol-1) remains incorrect. Thanks, Dwey ++ g_bar ver 4.5.7, md0.05.xvg: 0.0 - 5000.0; lambda = 0.050 foreign lambdas: 0.050 (250001 pts) 0.000 (250001 pts) 0.100 (250001 pts) md0.15.xvg: 0.0 - 5000.0; lambda = 0.150 foreign lambdas: 0.150 (250001 pts) 0.100 (250001 pts) 0.200 (250001 pts) md0.1.xvg: 0.0 - 5000.0; lambda = 0.100 foreign lambdas: 0.100 (250001 pts) 0.050 (250001 pts) 0.150 (250001 pts) . . . g_bar ver 4.5.5 or 4.6.2, md0.05.xvg: 0.0 - 5000.0; lambda = 0.05 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0 (250001 pts) delta H to 0.1 (250001 pts) md0.15.xvg: 0.0 - 5000.0; lambda = 0.15 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0.1 (250001 pts) delta H to 0.2 (250001 pts) md0.1.xvg: 0.0 - 5000.0; lambda = 0.1 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0.05 (250001 pts) delta H to 0.15 (250001 pts) . . . On 6/21/13 11:07 AM, Dwey wrote: 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,
