[gmx-users] question about image

David spoel at xray.bmc.uu.se
Fri Mar 19 21:35:01 CET 2004

On Fri, 2004-03-19 at 21:03, Weihua Guo wrote:
> Hi gmx-users,
> I have two peptides binding together, centered in the box and solvated as 
> my starting point. Now after several nanoseconds they drifted close to the
> side, and suddenly one chain sticks out of the box and get imaged in the
> other direction. I am sure it is due to image. They are imaged
> seperately during the run. I viewed the pdb file generated by "editconf -f
> x.gro -o x.pdb" with rasmol. (I used octahedron box and it showed me a
> cubic box though)
> My question is: Is the dynamics (energy terms etc) still correct? If it
> is, how should I treat the x.gro file in order for rasmol to show the
> actual orientations? 
Yes it is fine. Of course they can separate if that is energetically
favorable. You can make a traj containing only the peptides together by
trjconv -pbc cluster

> Thanks,
> Weihua
> Weihua Guo
> Department of Chemistry
> The University of Chicago
> 5735 S Ellis Ave 
> Chicago, IL 60637
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David van der Spoel, PhD, Assist. 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	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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