[gmx-users] question about image

[Weihua Guo]

So for example, if I calculate the distance between two peptides, it will
give me the correct (short distance between one peptide in one box 
and another in the adjacent box), rather than a long distance across
the same box? And the two peptides shown in the same box by rasmol
actually do not see each other through dynamics calculations? 

That would be great.

Thanks,
Weihua


 On Fri, 19 Mar 2004, David wrote:

> 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
> running
> trjconv -pbc cluster
> 
> > 
> > 
> > Thanks,
> > Weihua
> > 
> > 
> > 
> > Weihua Guo
> > Department of Chemistry
> > The University of Chicago
> > 5735 S Ellis Ave 
> > Chicago, IL 60637
> > 
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> -- 
> David.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 


Weihua Guo
Department of Chemistry
The University of Chicago
5735 S Ellis Ave 
Chicago, IL 60637