[gmx-users] RV: pregunta per la gromacs list

Berk Hess gmx3 at hotmail.com
Tue May 31 09:19:29 CEST 2005

You can not just use the original configuration.

The conversion for Gromos mentioned in editconf should work
fine. The molecule might look weird afterwards in some way.
But I don't know how it looks like in your case.
You can try adding the -c option to editconf to recenter
the molecule after rotation.


>From: "David L. Bostick" <dbostick at physics.unc.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] RV: pregunta per la gromacs list
>Date: Mon, 30 May 2005 16:04:13 -0400 (EDT)
>I've never simulated in truncated octahedral geometries before, but could
>you try restarting from the configuration without rotating? Shouldn't the
>water molecules lying outside the simulation cell boundaries be
>automatically wrapped around and relocated in the box?  In princible it's
>all bulk water right? ... as long as you give the appropriate dimensions
>for the unit cell?
>David Bostick					Office: 262 Venable Hall
>Dept. of Physics and Astronomy			Phone:  (919)962-0165
>Program in Molecular and Cellular Biophysics
>UNC-Chapel Hill
>CB #3255 Phillips Hall				dbostick at physics.unc.edu
>Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
>On Mon, 30 May 2005, Jordi Camps wrote:
> > On behalf of one of my work mates:
> >
> > Hi I'm trying to convert a restart file from amber to gromacs. I'm using
> > truncated octahedric box of water and I'm not able to convert the
> > orientation of the box from amber to gromacs. I know that amber applies 
> > rotation after the box construction (amber constructs octahedric boxes 
> > a cubic box and cutting off the corners), this rotation is done in order 
> > orientate that box for pme calculations, this rotation is 45º around Z 
> > 90 º around X axis and 35.264 around Y axis.
> > I've tried to apply reverse these rotations with editconf but it does'nt
> > work. I've applied other transformations (like the transformation 
> > in editconf help for gromos structures but any succesful result is 
> >
> > When I'm trying to visualize my original molecule or rotated ones in the 
> > rect option in trjconv very weird results are obtained.
> > Any hint or suggestion, thanks a lot in advance
> >
> >
> > --
> > Carles Ferrer-Costa				tel +34934037155
> > Molecular Modelling and Bioinformatics		fax +34934037157
> > IRBB-Parc Cientific de Barcelona. UB		e-mail:gandalf at mmb.pcb.ub.es
> >
> > Josep Samitier, 1-5 08028 Barcelona.
> >
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