[gmx-users] new OPLS-AA dihedral parameters for hydrocarbons ?
ester.chiessi at uniroma2.it
Thu Mar 1 11:05:49 CET 2012
I was checking the OPLS-AA dihedral terms for modeling an alcohol-like
I plotted the torsional energy for the dihedrals formed by these atomtypes:
CT CT CT HC,
CT CT CT CT,
HC CT CT HC,
CT CT CT OH,
OH CT CT HC
using the parameters in the OPLS-AA ffbonded.itp file of GROMACS library.
Then I plotted the same functions taking the (corresponding) dihedral
parameters from the Supporting Information of the original OPLS-AA
paper of Jorgensen (J. Am. Chem. Soc. 118, 11225-11236 (1996)).
The plots with the two series of parameters are very similar, but not
identical. For example:
1) for CT CT CT HC, the barrier between minimum energy states is about
0.2 kJ/mol higher using the Jorgensen 1996 parameters (in comparison
to OPLS-AA ffbonded.itp parameters)
2) for CT CT CT CT the barrier across cis state is about 1 kJ/mol
higher using the Jorgensen 1996 parameters
3) for HC CT CT HC, the barrier between minimum energy states is about
0.03 kJ/mol higher using the Jorgensen 1996 parameters
4) for CT CT CT OH the functions differ for an additive costant
(therefore they are equivalent)
5) only for OH CT CT HC the functions are identical.
In the dihedral section of ffbonded.itp file I found this comment:
; hydrocarbon *new* 11/99
I am wondering about which is the origin of the OPLS-AA dihedral
parameters for hydrocarbon molecules reported in ffbonded.itp. Is
there a later paper (1999 ?) where these variations are discussed?
My question rises since I have to decide the most proper dihedral
parametrization in OPLS-AA force field for my molecule.
Thanks in advance
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
Via della Ricerca Scientifica
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