[gmx-users] question about image

[David]

On Sat, 2004-03-20 at 00:49, Weihua Guo wrote:
> 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? 
If they are bound in the beginning they probably stay together. Hence,
if they are close there are non-bonded interaction, Lennard Jones and
Coulomb. In other words they do see each other


> 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
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> > -- 
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > _______________________________________________
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> > 
> 
> 
> 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
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-- 
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
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