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/[email protected]/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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
