yes, all angles and dihedrals are present but wath I mean is for example the
sp2
carbon of carbonate ion, I only need 2 angles to completely describe the
in-plane motion of the 3 oxygen atoms. Is correct to include all three in
plane coordinates?, What possible differences in the result from the MD
calculation
could be between one or the other situation?.
Thanks in advance!
> Date: Wed, 16 Jun 2010 12:52:32 +0200
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] redundancies in the .itp file
>
> On 2010-06-16 00.50, Víctor Bahamonde wrote:
> > Dear users
> >
> >
> > I have created a .itp file with the program TopolGen, published in the
> > website of GROMACS. to review the angles, I see that there are
> > redundancies. This will affect the results of molecular dynamics
> > calculation?. What should I do with them? (delete?)
> Yes. You have to review any such topology carefully. Please check
> whether all angles and dihedrals (in particular impropers) are present
> as well.
> > Thanks in advance!
> >
> >
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
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