I was wondering what happens if I use angle restraints, for example. Would it lead to an unstable simulation? I have seen that some people use some approximations, such as virtual sites to treat with linear molecules. I suppose that if people use this type of approximations instead of applying angle restraints, there should be problems with this approximation...is this correct? Which type of problems could be found?
Thanks a lot in advance,
Rebeca
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
> Date: Thu, 12 Feb 2015 07:27:32 -0500
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] alkynes in GAFF
>
> On Thu, Feb 12, 2015, Rebeca García Fandiño wrote:
>
> > I am trying to simulate an organic molecule containing an alkyne, using
> > GROMACS and the GAFF force field.
> >
> > The resulting structure from MD simulations is not correct, since the
> > triple bonds should be linear (C-C=C-H), and I observe an angle among
> > the atoms involved.
>
> What is the angle you see? What angle do you get if you minimize the
> structure? Linear molecules can be difficult for molecular mechanics force
> fields, since the angle force becomes poorly defined near 180 degrees.
>
> ...dac
>
>
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Received on Thu Feb 12 2015 - 14:00:02 PST
