> On 9/2/13 9:43 PM, Jernej Zidar wrote: >> 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 latter number, of course, is not an actual final answer. You have to do > a > corresponding gas-phase calculation to determine the real DG of solvation.
I see. I'll do a gas-phase calculation as well. > >> 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" ? >> > > I think a bigger factor is flexibility. For a relatively rigid, conjugated > system, it may not be a big issue. Gut feeling? Yes, I'd say that something > with 161 atoms is relatively large. > The polymer molecules is indeed very flexible.
-- 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
