[gmx-users] MM dihedral scanning

Justin Lemkul jalemkul at vt.edu
Fri Jan 13 04:40:18 CET 2017

On 1/12/17 10:29 PM, Mohsen Ramezanpour wrote:
> I was thinking of a potential solution for this.
> Please let me know your opinion as expert. Sorry, if it seems stupid :-)
> I have the QM scan profile already.
> 1-4 interactions for this dihedral must be included in charmm36.
> My idea:
> I was thinking to find the dihedral parameters *purely mathematically* (by
> using the dihedral potential function), so that the fitted mathematical
> curve will match as much as possible to the QM one.

Any dihedral of any form is just a cosine series.  That doesn't necessarily 
inform on the potential energy of the entire molecule.

> This should be doable by including more terms in dihedral fitting and
> playing with force constants, multiplicity, and angles.* BUT*, this time, I
> will exclude the 1-4 interactions *in this specific dihedral* when I am
> doing my simulations using charmm36.
> I think this approach might work. However, I am not sure if that is okay to
> exclude one specific dihedral in all the molecules of system (in all lipids
> of a bilayer) while other 1-4 are included (as it is the case for charmm36
> ff).

Dihedrals are by definition the term that compensates for errors in 1-4 terms 
due to defects in the additive nonbonded approximation.  The phase and 
multiplicity are generally apparent from looking at the number and position of 
minima.  The phase angle is generally not freely tunable; it should be 0 or 180 
for transferability.  Most of the fitting is just in the force constant. 
Kenno's program does this kind of stuff for you.  Don't try to reinvent the 
wheel - there's a several-decade precedent for CHARMM parametrization for a 
reason :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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