[gmx-users] Atom types for phosphate group in OPLS-AA force field
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 26 18:19:03 CEST 2012
On 4/26/12 12:15 PM, Delmotte, Antoine wrote:
> 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?
There is a large database at http://virtualchemistry.org/index.php but I don't
know if there will necessarily be anything similar to what you're looking for.
> Best regards,
> 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
>>> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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