[gmx-users] Morse potential conversion.

[Justin Lemkul]

On 3/10/15 7:51 PM, Dan Sponseller wrote:
> Hello GMX list.
>
> I am using the morse potential and I know that grompp converts the bonds from the harmonic potential to the morse potential at that time. From the equations 4.39 to 4.44 in the gromacs 5 manual, I can safely conclude that the bottom of the well is defined at Vm=0.0 so that with the first order approximation to the exponential term, we recover the Harmonic bond potential. This is fine, but it does not actually show how to get the three parameters needed for the morse potential from the two parameters listed in the force fields.
>
> Now the ffbonded.itp files do have an additional number listed but it is on the comment line below the bond definitions. Example:
> #define gb_1        0.1000  1.5700e+07
> ; H  -  OA      750
>
> Would the 750 be Dij, the disassociation energy? I doubt grompp is reading this off a comment line.
>

The dissociation energies are read from edissoc.dat in $GMXLIB.  The comment 
lines in ffbonded.itp from GROMOS are some type code or something.

> Does anyone have any insight into how grompp converts the bonds to morse. Any help would be appreciated.
>

Check out the source code in src/gromacs/gmxpreprocess/tomorse.c

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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