[gmx-users] Atom types for phosphate group in OPLS-AA force field

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 26 17:55:01 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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