Pressure coupling with a single molecule (i.e. in the gas phase) doesn't sound workable to me.
Mark On Wed, Sep 11, 2013 at 11:28 AM, Jernej Zidar <jernej.zi...@gmail.com> wrote: > Dear Justin, > > I followed your advice and started a gas-phase simulation. I removed the > solvent and simulated only the polymer molecule but I ended up with this > error: > One of the box vectors has become shorter than twice the cut-off length or > box_yy-|box_zy| or box_zz has become smaller than the cut-off. > > What can I do to remedy this? > > Thanks in advance, > Jernej > > On 4. sep. 2013, at 09:55, Jernej Zidar <jernej.zi...@gmail.com> wrote: > >> >>> 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 -- 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
