On 9/6/13 2:11 PM, prateekj wrote:
Hi,
I am trying to build itp file for polymer simulations using OPLS-AA and had
two questions I could not find a clear answer from the forum or the manual.
1. Is the order of bond types listed in a row of the [dihedral] section
important, i.e. if I replace ijkl by lkji, will this make any differences.
In principle, no, but you can convince yourself of this fact with a simple
single-point energy calculation.
Since type 3 is the RB dihedral, I see that the form sum_n C_n (cos(psi))^n
is unchanged with a transformation psi=-psi (or dihedral angle, phi=-phi)
but not sure. Note that I explicitly list the dihedral parameters for some
of the rows in the itp file, when the default parameters do not exist in
ffbonded.itp (in somewhat ad-hoc way for the moment by finding the closest
existing set. comments?).
Dihedrals are often not very transferable; proceed with caution.
2. Should I have 1-4 exclusions listed in [ pairs ] section for OPLS-AA? I
find conflicting statements when I searched on this. For example,
methanol.itp file in the OPLS-AA force-field directory lists the exclusions.
My understanding has always been what is in manual section 4.2.12, in which case
pairs are used for OPLS-AA, but not for other force fields like GROMOS (but only
in the case of alkanes). You can set up a test system with pdb2gmx and a simple
.rtp entry to see what it generates. The code should adhere to the force field
standard.
-Justin
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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