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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Received on Fri May 16 2014 - 21:00:03 PDT
