[gmx-users] comm-mode = Angular

[Tsjerk Wassenaar]

Hi Abu,

Indeed. You have to add a parameter rototr = yes. Note that the changes in
the .tpr file make it impossible to use these .tpr with other versions of
gromacs and vice versa. Besides, you need a reference structure for the
removal of the rotation/translation. This file has a fixed name:
ref_conf.gro. The best thing to do is to take the .tpr file for the
simulation and use editconf with an index file to generate ref_conf.gro from
this .tpr (using the desired set of atoms).

If you run into any trouble, please let me know. However, I'm rather busy at
this moment, so trouble shooting may take a while.

Good luck,

Tsjerk

On 4/26/06, Naser, Md Abu <mn2 at hw.ac.uk> wrote:
>
>  Hi Tsjerk,
>
> Thanks for  the link. I have been wondering how to select roto-translation
> option. Is it in the mdp file?
>
> With regards,
>  Abu Naser
>
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: mn2 at hw.ac.uk
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
>
>
>
>
> ------------------------------
> *From:* Tsjerk Wassenaar
> *Sent:* Wed 26/04/2006 12:05 PM
>
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] comm-mode = Angular
>
> Hi Abu,
>
> In fact, I have it implemented in two versions (3.1.4 and 3.2.1), but
> haven't contributed it to the official code yet. At this point I don't have
> the time either :S However, you can download my versions at
> http://md.chem.rug.nl/~tsjerk/GMX/ <http://md.chem.rug.nl/%7Etsjerk/GMX/>
>
> Cheers,
>
> Tsjerk
>
> On 4/26/06, Naser, Md Abu <mn2 at hw.ac.uk> wrote:
> >
> >  Hi Tsjerk,
> > I have been wondering whether Andrea Amadei  and coworkers' method (
> > J. Chem. Phys. 112(1) pp. 9-23) has been implemented in Gromacs yet.
> >
> > With regards,
> >
> >
> >  Abu Naser
> >
> > School Of Life Sciences
> > Heriot-Watt University
> > Edinburgh EH14 4AS
> > Email: mn2 at hw.ac.uk
> > Phone: +44(0)1314518265
> > Fax : +44(0) 131 451 3009
> >
> >
> >
> >
> > ------------------------------
> > *From:* David van der Spoel
> > *Sent:* Tue 25/04/2006 7:32 PM
> > *To:* Discussion list for GROMACS users
> > *Subject:* Re: [gmx-users] comm-mode = Angular
> >
> > Naser, Md Abu wrote:
> > > Hi All,
> > >
> > > Dose anyone know any literature regarding comm-mode = Angular option?
> > it just sets the overall angular momentum to zero.
> >
> > > With regards,
> >
> > > Abu Naser
> > >
> > > School Of Life Sciences
> > > Heriot-Watt University
> > > Edinburgh EH14 4AS
> > > Email:
> > mn2 at hw.ac.uk <mailto:mn2 at hw.ac.uk>
> > > Phone: +44(0)1314518265
> > > Fax : +44(0) 131 451 3009
> > >
> >
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
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> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> >
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se
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>
> --
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
>
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>


--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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