[Molecularmechanics] Re: Some general remarks.
Martin Field
molecularmechanics@tddft.org
Wed, 19 Nov 2003 17:48:57 +1300
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Hi all,
I've been reading the posting on the list
with interest and have a couple of remarks.
Currently, it seems that the emphasis of
the discussion is upon how to specify the
composition of the system in terms of fragments
or molecules. This is because dealing with
force-fields has been deemed too complicated
(at least for the moment).
Clearly both problems are important, but
it would seem to me that tackling the force-field
problem is in some ways easier than the composition
problem and that the latter could have a more immediate
impact in the MM area.
Some points (and questions):
1. Specifying composition is not a problem unique
to MM simulations. Conventions to do so already exist
and no doubt there are ongoing efforts as well.
How much overlap is there with these?
2. Is a unique convention desirable? Thus, for example,
a PDB or a CIF-like convention may be most appropriate
for biomolecule people but other conventions may be
more suitable in other areas.
3. Most simulation programs that I am familiar
with generate explicit lists of atoms, force-field
terms, force-field parameters, etc. when they
generate a force-field for a particular system.
Most of these can also write and reread this
information so that the force-field generation
step does not have to be repeated.
I think it would be a useful first step and
relatively straightforward to come up with a
(XML) representation of this data. To be more
concrete, a file or files that do the same thing
as AMBER top files or CHARMM psf and parameter
files.=20
Any comments?
Cheers,
Martin Field.
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<DIV><BR>Hi all,</DIV>
<DIV> </DIV>
<DIV> I've been reading the posting on the list<BR>with =
interest and=20
have a couple of remarks.</DIV>
<DIV> </DIV>
<DIV> Currently, it seems that the emphasis of<BR>the =
discussion is=20
upon how to specify the<BR>composition of the system in terms of =
fragments<BR>or=20
molecules. This is because dealing with<BR>force-fields has been deemed =
too=20
complicated<BR>(at least for the moment).</DIV>
<DIV> </DIV>
<DIV> Clearly both problems are important, but<BR>it would =
seem to=20
me that tackling the force-field<BR>problem is in some ways easier than =
the=20
composition<BR>problem and that the latter could have a more =
immediate<BR>impact=20
in the MM area.</DIV>
<DIV> </DIV>
<DIV> Some points (and questions):</DIV>
<DIV> </DIV>
<DIV>1. Specifying composition is not a problem unique<BR> =
to MM=20
simulations. Conventions to do so already exist<BR> and no =
doubt=20
there are ongoing efforts as well.<BR> How much overlap is =
there=20
with these?</DIV>
<DIV> </DIV>
<DIV>2. Is a unique convention desirable? Thus, for =
example,<BR> a=20
PDB or a CIF-like convention may be most appropriate<BR> for =
biomolecule people but other conventions may be<BR> more =
suitable in=20
other areas.</DIV>
<DIV> </DIV>
<DIV>3. Most simulation programs that I am familiar<BR> with =
generate explicit lists of atoms, force-field<BR> terms, =
force-field=20
parameters, etc. when they<BR> generate a force-field for a=20
particular system.<BR> Most of these can also write and =
reread=20
this<BR> information so that the force-field=20
generation<BR> step does not have to be repeated.</DIV>
<DIV> </DIV>
<DIV> I think it would be a useful first step =
and<BR> =20
relatively straightforward to come up with a<BR> (XML)=20
representation of this data. To be more<BR> concrete, a file =
or=20
files that do the same thing<BR> as AMBER top files or =
CHARMM psf=20
and parameter<BR> files. </DIV>
<DIV> </DIV>
<DIV>Any comments?</DIV>
<DIV> </DIV>
<DIV>Cheers,</DIV>
<DIV> </DIV>
<DIV>Martin Field.<BR></FONT></DIV></BODY></HTML>
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