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

Justin Lemkul jalemkul at vt.edu
Tue Sep 3 03:57:42 CEST 2013

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.

>    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.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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