[gmx-users] changing atom types versus adding dihedrals to atom types

Justin Lemkul jalemkul at vt.edu
Thu Sep 12 01:57:07 CEST 2013

On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
> Hi all,
> in another thread it was recommended that instead of changing the atom
> types by analogy to ones with the desired parameter already assigned, that
> instead one should assign bonded parameters by analogy.  I was just
> wondering how this is better?

I didn't suggest that.  I said that any assignment by analogy can have negative 
outcomes.  Bonds and angles, in theory, are a bit easier to deal with because 
the nonbonded interactions between their atoms are excluded.  Torsions are very 
difficult because the torsional bonded terms have to be balanced against the 
charge and LJ parameters of atoms separated by 3 bonds, i.e. 1-4 interactions.

Let me state very clearly that, for any missing parameters, anything short of a 
thorough parametrization and validation is (in my purist mind) unsound.

>   As long as the atom type isnt too different, then why would the torsions
> not work out right? If the parameters are interrelated, what makes it
> better to add one term to an atom type rather than changing all the terms
> (to ones that are supposed to be together)?

The key is being sufficiently similar, but even subtle differences between LJ 
parameters have very large consequences, especially for 1-4 interactions, so I 
find it hard to believe that one will recapitulate accurate interactions in this 
case.  Of course, all assignments by analogy bear some penalty for nonequivalent 
groups.  I balked at your initial post in the other thread because there was no 
need to mess with atom types.  The system at hand there contained protein and 
lipid and could be completely described by existing atom types and bonded types, 
the OP there was just (and perhaps still is) constructing the force field 
incorrectly.  I felt it need to be stated that the approach there would not 
necessarily be productive, and to make sure the archive was complete so that no 
one would come across a post in vacuum and assume that he or she can simply swap 
around atom types to make error messages go away.  Your initial statement 
referred only to bonds and angles, which indeed would be insensitive to changes 
in LJ parameters on any of those atoms, but since the thread was in the context 
of dihedrals, I thought I should state my opinion there.



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

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


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