[gmx-users] Constraints only on Backbone

[Justin A. Lemkul]

Quoting Bjoern Olausson <bjoern.olausson at biochemtech.uni-halle.de>:

> Hi all,
>
> first of all, I am new to gromacs ... (trying to switch from amber to
> gromacs)
> as you can see from the following qestion:
>
> Is  there a way to apply constraints only to the backbone of my Proteine and
> let the sidechains "shake" (LINCS)

Do you mean constraints or restraints?  These are different ideas in Gromacs. 
Using LINCS or SHAKE would mean applying constraints to your sidechains, so I
don't understand the question.

If you want to apply constraints to the backbone atoms only, you can define them
explicitly in your topology and set 'constraints = none' in your .mdp file.

If you want to apply restraints to the backbone atoms only, you can create a
posre.itp file from genpr.

-Justin

>
> I successfully ran a simulation, but only managed to put constraints on
> everything or no constraints at all.
>
> Would be great if someone could show me an example.
>
> kind regards
> Bjoern Olausson
>
> --
> Bjoern Olausson
> Martin-Luther-University Halle-Wittenberg
> Institute of Biochemistry/Biotechnology
> AG Molecular Modeling
> 06099 Halle, Germany
> Phone: +49-345-5524863
> Fax: +49-345-5527011
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========================================

Justin A. Lemkul
Graduate Research Assistant
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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