[gmx-users] OPLS-AA force field again regarding 1-4 interaction
alokjain at iitk.ac.in
alokjain at iitk.ac.in
Mon Sep 11 20:00:44 CEST 2006
Thanks David for your reply, I have a another doubt on OPLS force field
regarding 1-4 interaction.
In manual (chapter 4 page no 62) it was written The use of RB potential
implies exclusion of LJ interaction between first and the last atom of the
dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14
energy in my log file (see below) is there is any problem in this
simulation or it is normal?
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
and what I understood from articles on OPLS force field that it scale down
the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
what about GROMOS96 force field, it is mention in manual (Chapter 4 page
no 75) it also scale down the LJ-14 repulsion term .
what I understood by manual that It uses separate parameter for LJ-14
interaction Is it is correct? If yes then It uses separate parameters only
for LJ repulsive term or all the non bonded terms i.e. LJ repulsive,LJ
attractive and for coulomb term?
> 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
>> they have different formula for calculating the torsion angle
>> I think that is Ryckaert-Bellemans function, but there is no separate
>> 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
>> -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
>> ; 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 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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