Hi everyone, I'm having problems when calculating Free energy through the g_bar tool. I'm trying to decouple separately the electrostatic and the Vdw terms. So, after performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1 steps: 0.0-0.1-0.2...0.9-1.0) and the same for the LJ-terms, I'm applying the g_bar for all md*.xvg output files, from both decoupling steps, all together. I mean I join the md*.xvg files from the two decouplings and apply g_bar only once. As a result I'm getting a warning message informing that some results violate the Secong law of Thermodynamics and the error estimation is about 8 KJ/mol! On the other hand, when I apply the g_bar tool separately for the two decouplings I no longer "violate the Second Law" and the errors are more feasible (~0.3 KJ/mol), however I don't know how the join the two results in order to get the solvation Free energy of the whole process (considering that this is possible, I don't know this as well).
Any idea? Daniel. -- View this message in context: http://gromacs.5086.n6.nabble.com/Solvation-Free-Energy-calculation-g-bar-tp4998662.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
