Dear all,<div><br></div><div>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".</div><div>In one of those dwellings, I came across an older post [<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg42568.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg42568.html</a>] which reads:</div>
<div><br></div><div><div>Question:</div><div>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.</div>
</div><div>Answer:</div><div><br></div><div>So, my question, if a question at all:</div><div><br></div><div>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" ?</div>
<div><br></div><div>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 ?</div>
<div><br></div><div>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.</div>
<div><br></div><div>All the best,</div><div>Ed.</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div>