Thank you very much for your answer. This has been very helpful. I think
I will follow your advice and try to find similar molecules to find the
parameters.
Could I just ask you if you know of a database where I could look for
the opls parameters which have calculated for other molecules?
Best regards,
Antoine
On 26/04/12 16:55, Justin A. Lemkul wrote:
On 4/26/12 11:37 AM, Delmotte, Antoine wrote:
Dear Justin,
Many thanks for your response. I managed to reduce the number of
errors by
trying other atom types, by looking at what seemed most likely to be
right from
the ffnonbonded.itp and ffbonded.itp files.
Unfortunately, I did not manage to find a combination that both made
some sense,
and allowed to remove the errors. So I guess these things need to be
parametrized, as you said.
Could you possibly let me know if there is a relatively easy and
straightforward
way to find these parameters? (I guess the answer is probably "no",
but it's
always worth asking, I guess...)
You can make a first effort by assigning parameters based on existing,
similar, parameters. They may or may not exist.
I also noticed that there is a option "-zero" in grompp which "Sets
parameters
for bonded interactions without defaults to zero instead of
generating an error".
What does it mean exactly? Is it just taking the angles and distances
inferred
from the structure as the ones at equilibrium? Is it safe to use it?
What it means is "ignore the problem and simply assign the value of
zero for equilibrium lengths, force constants, etc."
I am just a beginner with MD, and I just want to do a quick run to test
something. I have no need for super high accuracy, and the run I want
to try
will be very small (maybe 1 or 2 ns, or something like that), and for
a very
large system (~80 000 atoms). Would that be unreasonable to use that
"-zero"
option (it is tempting, I must say...)?
I say that using -zero is a bad idea. It ignores the problem and
whatever results you obtain would be questionable, at best.
Parameterization of novel species is an advanced topic. Most people
will spend several months developing good parameters for a new residue
or molecule.
-Justin
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