The system in you topology must be complete even for QMMM, so you'll
need FF parameters also for the QM part.
Partition models for QM/MM work with the following energy decomposition:
E(total) = E(QM_system) + E(MM_system) + E(QM-MM interaction)
E(QM_system) and E(MM_system) are easy to define (computed at QM and MM
levels respectively), but E(QM-MM interaction) is a bit more involved.
One way to account for this interaction energy is through the ONIOM (and
the like) partition scheme:
E(total) = E(QM_system@QM level) + E(whole_system@MM level) -
E(QM_system@MM level)
So, you need to evaluate the whole system at MM level and that's why you
need a force field for this part as well. Anyway, I think that for the
QM_system tretaed at MM level only nonbonded interactions mater, since
bonded interactions (that are not involved with the boundaries) are
cancelled out when performing this subtraction: E(whole_system@MM level)
- E(QM_system@MM level). For that reason, I think that bonded parameters
that are not present in the boundaries, are not relevant and could be
omitted in the topology.
Javier
El 08/06/12 01:47, Justin A. Lemkul escribió:
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
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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