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

Gerrit Groenhof ggroenh at gwdg.de
Fri Jun 8 15:49:10 CEST 2012


INdeed, you would still need a LJ term for the QM atoms, in order to interact with the MM atoms. Only if the radius around your special atom were larger than the LJ cut-off could you safely ignore the LJ paramter.


> Message: 3
> Date: Thu, 07 Jun 2012 19:47:02 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] qmmm and "real-life" meaning of null
> 	lennard-jones	parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FD13D76.9040307 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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:
> http://pubs.acs.org/doi/abs/10.1021/ja00824a004
>> 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
> -- 
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================

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