[gmx-users] Dihedral angle in OPLS-AA force field

[David van der Spoel]

alokjain at iitk.ac.in 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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