[gmx-users] redundancies in the .itp file

[Justin A. Lemkul]

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: spoel at xray.bmc.uu.se
>  > To: gmx-users at gromacs.org
>  > 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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