Dear Justin, I set the couple_intramol parameter to yes and rerun the free energy simulations. mdrun was able to fully utilize all the cores in the system but there's one issue. The free energy of solvation is vastly different if the parameter is set to 'no' (DG=-408.10 +/- 8.69 kJ/mol) or 'yes' (1890.14 +/- 15.52).
The behavior observed in the simulations is more consistent with the latter number. The manual states that 'yes' can be used can be "useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off." My molecule has 161 atoms. How large is "relatively large" ? Thanks in advance, Jernej Zidar On Thu, Aug 29, 2013 at 8:00 PM, <gmx-users-requ...@gromacs.org> wrote: > This issue is discussed very frequently, particularly in the context of free > energy calculations. Please refer to the list archive and consider the effect > that couple_intramol setting has on the DD setup. -- Windows: Re-Boot, Linux: Be-Root. -- 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
