Ok, I get it. I'm more 'familiar' with the truncated octahedron shape.
Thank you very much for all your answers.
Best regards,
KM
2015-08-07 15:18 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Fri, Aug 7, 2015 at 3:35 AM, Karolina Markowska
> <markowska.kar.gmail.com> wrote:
> > My 'weird' water isn't shown at any of your examples. It comes out, that
> my
> > 'weird' water was the 'triclinic' water. If I may ask, what's the utility
> > of that kind of water representation?
>
> The triclinic shape is what the actual unit cell looks like. You
> actually have to do some extra transformations to get the truncated
> octahedron shape (which is why 'image familiar' is slower than
> 'image'). So the triclinic shape is good for speed, while the
> truncated octahedron can be "nicer" looking.
>
> -Dan
>
> >
> > Thank you once again for your help.
> >
> > Best regards,
> > KM
> >
> >
> >
> > 2015-08-06 15:19 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
> >
> >> On Thu, Aug 6, 2015 at 7:35 AM, Karolina Markowska <
> >> markowska.kar.gmail.com>
> >> wrote:
> >>
> >> > Dear Amber Users,
> >> >
> >> > I have a problem with cpptraj and it's autoimage command. My system
> >> > consists of two chains and two Mn2+ ions. I usually use the script
> below,
> >> > but when I use it on this system, something went wrong.
> >> >
> >> > reference protein_complex.inpcrd
> >> > trajin emd2.traj.gz
> >> > center :1-374 mass origin
> >> > image origin center
> >> >
> >>
> >> These two commands are pointless here. Their effect is promptly
> >> overwritten by the "autoimage" command.
> >>
> >>
> >>
> >> > autoimage
> >> > rms ToRef :1-374.CA,C,N= reference out rmsd_prod.arg mass
> >> > atomicfluct out rmsf_prod.arg :1-374 byres
> >> > trajout protein_complex_f.binpos binpos
> >> > go
> >> >
> >> > I looks like only the first chain was centered. I've tried to change
> the
> >> > autoimage command and put:
> >> >
> >>
> >> Yes, this is how "autoimage" works. In some cases it can result in a
> >> waterbox that looks "shifted" compared to all of the chains, but I have
> >> usually found that it suffices for my needs. If you really want all
> chains
> >> to be centered in the box, then you should follow the "autoimage"
> command
> >> with separate center and image commands (the ones I told you were
> pointless
> >> above):
> >>
> >> autoimage
> >> center :1-374 mass origin
> >> image origin center familiar
> >>
> >> Note that the "familiar" here is because you are using a truncated
> >> octahedron ("autoimage" takes care of that distinction by default, but
> with
> >> the image command it's necessary). In this case, the "autoimage"
> command
> >> will properly image the different chains with respect to each other, and
> >> the following 'center' and 'image' commands will center all of the
> chains
> >> in the unit cell and image the waters around that.
> >>
> >>
> >> > autoimage anchor :1-374
> >> >
> >>
> >> If residues 1-374 are from a dimer (i.e., two distinct "molecules"),
> then
> >> this is not a good thing to do. If they are imaged in separate boxes,
> then
> >> this will prevent them from being imaged back into the same box.
> >>
> >>
> >> > because I've read in the Amber Manual, that autoimage by default
> center
> >> > only the first molecule, but after that the water box looked wierd.
> >> >
> >>
> >> You need to be more specific. There are a lot of ways that a water box
> can
> >> look "weird". Here are some examples:
> http://www.shaman.ibpc.fr/heat.png,
> >> http://ambermd.org/tutorials/basic/tutorial2/files/vmd_crdbox1.jpg
> >> (pretend
> >> that applies to waters), ... and it's impossible to know what people
> >> consider 'weird' and 'normal'.
> >>
> >> One guess I have is that it looks like "chunks" are cut out of the
> corners
> >> of the unit cell (like the first link I showed above), in which case
> that
> >> problem arises because you did not use NpT to equilibrate the density,
> >> leading to fictitiously low pressures and a simulation that is actually
> >> *boiling* as a result. If I am mistaken, you would need to see an
> image so
> >> we can see what you see.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Fri Aug 07 2015 - 14:00:02 PDT
