Hi Mark,
By "missing", I meant zero by design. I found the initial opls paper in
which the H atom in ammonia is assigned a zero LJ parameter and the
entire LJ parameter for ammonia is assigned to the N atom.
I was just wondering if assigning the entire LJ parameter to the N atom
might affect the adsorption of the polar ammonia molecule within the MD
model since instead of there being four potential energy wells in the
ammonia molecule, there would only be one potential energy well and this
single well may not interact as significantly with the multiple
potential energy wells present at the edge of the hydrogen terminated
graphene sheet. Just looking for your comments and thoughts.
Thanks.
Darrell
Date: Sun, 01 Nov 2009 18:20:26 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4aed36ba.1040...@anu.edu.au>
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Darrell Koskinen wrote:
Hi Mark,
I thought opls_127 and opls_128 were the representative atoms to use for
ammonia. Please correct me if I am wrong.
I don't know anything more than what's in ffoplsa* files or the papers.
Would the adsorption of the polar ammonia molecule onto the polar
(hydrogen-terminated) edges of the graphene sheet be affected by the
missing LJ parameter on the H atoms?
Define "missing". If it is zero by design, that's because zero served
the purpose during the parameterization, and the documentation as quoted
by you is perhaps erroneous with respect to small molecules. If it
oplsa_128 should have non-zero LJ then you'll need to find more evidence
of that in the OPLSAA papers, or by consulting the authors. Note that
most models of water do not have LJ on the H atoms, and so not having LJ
on H atoms of solvated ammonia is probably quite consistent.
Doesn't this bring us back to the point of quite a while ago, that an
ammonia model that was probably not parameterized for the gas phase
might not be useful in the gas phase?
Mark
Date: Mon, 26 Oct 2009 08:47:14 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4ae4c762.2060...@anu.edu.au>
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Justin A. Lemkul wrote:
Darrell Koskinen wrote:
I looked through the ffoplsaanb.itp file and see that all the H
atoms except for the following four have zero LJ parameters:
HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine & Guanine H-C2
However, in the paper "Development and Testing of the OPLS All-Atom
Force Field on Conformational Energetics and Properties of Organic
Liquids", it states: "The original OPLS (optimized potentials for
liquid simulations) potential functions used a partially united-atom
(UA) model; sites for nonbonded interactions are placed on all
nonhydrogen atoms and on hydrogens attached to heteroatoms or
carbons in aromatic rings". Later, the paper indicates that the
paramters were adopted as much as possible from the OPLS-UA force
field. Thus, since "sites for nonbonded interactions are placed on
hydrogens attached to heteroatoms ", it appears to me that a site
for a non-bonded interaction should exist on the H atoms within
ammonia. Is my interpretation incorrect?
I don't think so. Each of the above examples you've cited above is
for a C-H bond in an aromatic ring. In OPLS, all N-H bonds involved
hydrogen atoms with zero LJ parameters. See, for example, any
backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will
see the atom types used.
I think you're both partly wrong. Type 140 is not for C-H in an
aromatic ring, and if you grep 1.008 ffoplsaanb.itp you get many more
H atom types with LJ. Certainly Justin's right inasmuch as amide N-H
type 241 has no H LJ parameters. Perhaps there's other text that
Darrell hasn't found yet, or backbone nitrogen is not considered a
heteroatom :-).
Mark
Darrell
Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4adc1e3a.8010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi,
I see that the Lennard Jones parameters for the N & H atoms in
ammonia, represented by opls_127 and opls_128 in the file
ffoplsaanb.itp are:
opls_127 NT 7 14.00670 -1.020 A 3.42000e-01
7.11280e-01
opls_128 H 1 1.00800 0.340 A 0.00000e+00
0.00000e+00
Why are sigma and epsilon both zero for H? Are the LJ parameters
for H embedded in the parameter for NT? If so, how were these
parameters combined?
What do other H have? What do the OPLS-AA paper(s) have to say
about such H atoms?
Mark
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