[gmx-users] Atom ordering for RB dihedrals in OPLS-AA

[Justin Lemkul]

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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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