Víctor Bahamonde wrote:
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?.
I think you need all three. In theory, by defining two, the third should be set
because the geometry is fixed, but I think it will depend on whether or not
you're using constraints or a flexible model. By defining all the angles
explicitly, you leave nothing to chance.
-Justin
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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