[gmx-users] trjconv

[rams rams]

Hi Tsjerk,

It means the resulting trajectory is free from translational and rotational
degrees of freedom which I can use for the studies of internal dynamics i
suppose.

Ram.


On Wed, Sep 10, 2008 at 3:05 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ram,
>
> -fit rot+trans performs an ordinary least-squares fit using the
> reference structure provided with -s, removing rotational and
> translational degrees of freedom.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Sep 9, 2008 at 9:47 PM, rams rams <rams.crux at gmail.com> wrote:
> > Dear Users,
> >
> > I have a question about the option -fit in trjconv.
> >
> > The default option with -fit is none. If I use the option as rot+trans,
> does
> > it mean that the rotational and translational motions are removed from
> the
> > trajectory ? If not, is there any option in gromacs, to create a
> > translational and rotational free trajectory from the original trajecotry
> > file ? I also want to make sure the usage of the command:
> >
> > trjconv -f original trr -s .tpr -o rot_trans_free.trr -fit rot+trans
> >
> > Thanks in advance.
> >
> > Ram.
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
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> The Netherlands
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