[gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 8 01:47:02 CEST 2012

On 6/7/12 7:28 PM, Edward Deira wrote:
> Dear all,
> I'm currently starting to dwell deeper in MD, and I'm taking some time to
> understand what's going on inside the gromacs "black-box".
> In one of those dwellings, I came across an older post
> [http://www.mail-archive.com/gmx-users@gromacs.org/msg42568.html] which reads:
> Question:
> 4. In ffnonbonded.itp, why are both sigma and epsilon set to zero for HW
> (opls_117)? This seems to imply that, as far as Lennard-Jones interactions are
> concerned, the hydrogens on the waters don't exist. Or, in other words, in the
> absence of charges, the hydrogens don't "feel" the hydrogens, the hydrogens
> don't "feel" the oxygens, and the oxygens don't "feel" the hydrogens. In other
> words, the hydrogens interact with the world only via electrostatic (Coulombic)
> interactions. Is this a correct interpretation?Correct. Many force fields do this.
> Answer:
> So, my question, if a question at all:
> Suppose I have a regular protein and put inside some metal atom that will
> coordinate with some O and N atoms from the side chains. If the sigma and
> epsilon for that metal are null, than the metal - sidechains interactions are
> exclusively electrostatic. Does this make sense ? What are the implications of
> this for the "coordination chemistry" of that "metal - sidechain complex" ?
> On the side: suppose I want some non parameterized metal atom, say W, for which
> I will compute all the other parameters in the same/similar way described in the
> force field papers, but for which no experimental data are available for me to
> compare computable meaningful sigma and epsilon values. Can I just sigma and
> epsilon to zero ? Or should I do qmmm to have W in the qm part ?

The fact that the LJ parameters for H are zero derives from its size.  The 
environment is more strongly influenced by the heavy atom to which H is bonded. 
  In the case of a larger metal ion, I would seriously doubt that setting LJ 
parameters to zero is valid.  It's quite convenient, but in most force fields, 
all metal ions have some LJ parameters.  Perhaps investigating how those 
parameters were derived would be useful.  For what it's worth, I believe the 
origin of the zero-LJ H parameters comes from this work:


> Also, from the few tutorials and from the manual, I have the impression that
> even for qmmm with gromacs and mopac i still need force field parameters for the
> qm part, is this true ? Or i just need to include a qmmm section in all mdp
> files, including the first ion adding and energy minimization steps ? Sorry for
> the naivety in this, but i've only made "regular protein" MD so far.

I've never done any QM/MM, but my assumption would be that you have to have some 
valid topology to start with.  Perhaps someone else can comment on this 
methodological issue.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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