[gmx-users] Atom types for phosphate group in OPLS-AA force field
antoine.delmotte09 at imperial.ac.uk
Thu Apr 26 18:15:33 CEST 2012
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
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?
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
>> 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
>> 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
>> 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
>> 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.
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