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

David L. Bostick dbostick at physics.unc.edu
Mon May 30 22:04:13 CEST 2005


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 a
> rotation after the box construction (amber constructs octahedric boxes using
> a cubic box and cutting off the corners), this rotation is done in order to
> orientate that box for pme calculations, this rotation is 45º around Z axis
> 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 suggested
> in editconf help for gromos structures but any succesful result is obtained.
> When I'm trying to visualize my original molecule or rotated ones in the -ur
> 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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