[gmx-users] Re: MD vs. free energy simulations

Jernej Zidar jernej.zidar at gmail.com
Tue Sep 3 03:43:35 CEST 2013

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

  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-request at 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.

More information about the gromacs.org_gmx-users mailing list