[EMAIL PROTECTED] wrote:
Dear All,
I have a basic question on Dihedral angle in OPLS-AA force field.
I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is no separate term
for Improper dihedral term.
when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1
version (pdb2gmx option 3) I got following energy terms in my log file.
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01
so I am getting two proper dihedral term in output(Proper Dih. and
Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got
following comments
Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use improper for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), the are
; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment,
; to keep things compatible.
So its mean Proper Dih. which I am getting, In reality it is Improper
Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if
I am wrong).But in original OPLS force field Improper Dihedral was not
defined so how we can justify uses of Improper Dihedral.
yes that's correct. AFAIK proper dihedrals are used in OPLS for instance
for keeping rings flat.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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