[gmx-users] GAFF and alkynes

[Justin Lemkul]

On 2/12/15 9:43 AM, Rebeca García Fandiño wrote:
> Thanks a lot for the suggestions, Justin.
> In your CO2 tutorial I have seen the comment "One cannot effectively build this
> molecule in the traditional sense, as there are algorithmic reasons why
> an angle of 180° is not stable during a simulation."
>
> I was wondering what happens if I use angle restraints, for example. Would it lead to an unstable simulation? I suppose that if people use virtual sites to treat with linear molecules instead of applying angle restraints, there should be problems with this approximation...is this correct?

A restraint is just a biasing potential towards some desired outcome.  It's not 
necessarily even different in form from a normal harmonic interaction, but I'd 
be hesitant to try to use some angle definition and a restraint on top of that. 
  The GROMACS code indicates there is a linear angle potential, but it doesn't 
seem to be documented.  This was likely added to circumvent the previous 
problems with these linear species.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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