Thanks Brian, Jason,
Having tried various imaging commands in cpptraj and VMD, I'm concerned
there's something up with my system now. It seems as though the micelle is
straddling the periodic box in later stages of my production, and because
my RDFs/integrated RDFs are giving me intensities greater than the number
of ions in the actual box (60), I assume that it's a consequence of the
imaging confusing things as was suggested earlier in the thread. Especially
because when I turn imaging off (noimage) I end up with a totally flat
curve over the 0-10 Angstrom range, which doesn't make any sense given what
ambmask and VMD are telling me. I haven't turned wrapping (iwrap=1) on in
PMEMD, and when I run VMD on the coordinates prior to any adulteration, the
box from "pbc box" is seemingly arbitrarily way below the micelle and not
triclinic. If I image in cpptraj using something of the order "image
triclinic" I get something much more sensible-looking if I then visualise
that using the same procedure in VMD, but I still don't follow why the RDF
is the way it is.
I used the command:
radial rdf 0.1 10 :61-120 :SDS.S39 volume
Residues 61-120 are Na+ ions and changing the mask doesn't alter anything.
"SDS.S39" is the only mask that seems to work for the sulphur (S39) atom in
the "SDS" residue, which was originally adapted in tleap from a .mol2 file
I generated.
I've tried so many things that I think I may just be missing something
really obvious, so apologies if this is so, but I would really sincerely
appreciate any help.
Best regards,
Ben
On 17 May 2014 03:56, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, May 16, 2014 at 12:40 PM, Ben Ahmady <ahmady.ben.gmail.com> wrote:
>
> > Hi Brian,
> >
> > Thanks for your reply. I can only assume that the reference sites are
> > indeed near the boundary, which explains the discrepancies I'm seeing. I
> > think I've managed to make sense of cpptraj's radial function and getting
> > it to recognise my truncated octahedron and PBC correctly, but I'm having
> > trouble getting VMD to give me numbers of sodium ions within certain
> > regions/distances of sulphur atoms (in the surfactant) because I believe
> > that it too is getting conflicting information somewhere. That was why I
> > saved my "image familiar" (via ptraj) centred coordinates in NETCDF,
> > because I was getting the "diamond shaped holes" (which I read about
> here:
> > http://archive.ambermd.org/201006/0595.html) in other formats. The
> problem
> > is "pbc box" just gives me something orthorhombic so yes, I think you're
> > right that VMD can only handle those.
> >
>
> Actually this isn't quite right. VMD can handle arbitrary triclinic cells
> (truncated octahedron included). They key is that you have to use the
> pbctools plugin in order to get it to work.
>
> I'm not completely clear on the syntax, but I think you can do something
> like the following in the tcl commandline:
>
> pbc set -vmd -all <a> <b> <c> [<alpha> <beta> <gamma>]
>
> If you do not specify alpha beta or gamma, VMD will assume 90 degrees (a
> triclinic cell), but you are perfectly allowed to do 109.471 degrees for
> each angle to specify a truncated octahedron (the -all flag specifies to
> apply those periodic boundary conditions to all frames in the trajectory).
> You can also use the -first and -last flags to add the PBC information to
> only a subset of snapshots. This would really only be useful for constant
> pressure calculations, but it would become tedious to do a separate command
> for each snapshot in that case...
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ben Ahmady
Molecular Modelling & Materials Science (M3S) Centre
Department of Chemistry
University College London
http://www.m3s.ucl.ac.uk/
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Received on Sun May 18 2014 - 14:00:02 PDT
