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<DIV><FONT size=2 face=Arial><FONT size=3 face="Times New Roman">Dear
All<BR><BR>I was checking the OPLS-AA dihedral terms for modeling an
alcohol-like <BR>molecule.<BR><BR>I plotted the torsional energy for the
dihedrals formed by these atomtypes:<BR>CT CT CT HC,<BR>CT CT CT CT,<BR>HC CT CT
HC,<BR>CT CT CT OH,<BR>OH CT CT HC<BR>using the parameters in the OPLS-AA
ffbonded.itp file of GROMACS library.<BR><BR>Then I plotted the same functions
taking the (corresponding) dihedral <BR>parameters from the Supporting
Information of the original OPLS-AA <BR>paper of Jorgensen (J. Am. Chem.
Soc. 118, 11225-11236 (1996)).<BR><BR>The plots with the two series of
parameters are very similar, but not <BR>identical. For example:<BR>1) for
CT CT CT HC, the barrier between minimum energy states is about <BR>0.2
kJ/mol higher using the Jorgensen 1996 parameters (in comparison <BR>to
OPLS-AA ffbonded.itp parameters)<BR>2) for CT CT CT CT the barrier across cis
state is about 1 kJ/mol <BR>higher using the Jorgensen 1996
parameters<BR>3) for HC CT CT HC, the barrier between minimum energy states is
about <BR>0.03 kJ/mol higher using the Jorgensen 1996 parameters<BR>4) for
CT CT CT OH the functions differ for an additive costant <BR>(therefore
they are equivalent)<BR>5) only for OH CT CT HC the functions are
identical.<BR><BR>In the dihedral section of ffbonded.itp file I found this
comment:<BR>; hydrocarbon *new* 11/99<BR>I am wondering about which is the
origin of the OPLS-AA dihedral <BR>parameters for hydrocarbon molecules
reported in ffbonded.itp. Is <BR>there a later paper (1999 ?) where these
variations are discussed?<BR>My question rises since I have to decide the most
proper dihedral <BR>parametrization in OPLS-AA force field for my
molecule.<BR><BR>Thanks in advance<BR><BR>Ester<BR><BR></FONT></FONT><FONT
size=2 face=Arial>Ester Chiessi<BR>Dipartimento di Scienze e Tecnologie
Chimiche<BR>Università di Roma Tor Vergata<BR>Via della Ricerca
Scientifica<BR>00133 Roma<BR><A
href="http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm">http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm</A><BR>tel:
*39*6*72594462</FONT></DIV></BODY></HTML>