Hi, 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.
gerrit > > Message: 3 > Date: Thu, 07 Jun 2012 19:47:02 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] qmmm and "real-life" meaning of null > lennard-jones parameters > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fd13d76.9040...@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 > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
