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.
Is there any way I can determine the number of atoms/ions of a particular
mask within a region of another mask, (a la "$sel num" in VMD, after
setting "sel" to something like "'X' and within Y of name 'Z'")? Or will I
just have to re-run my coordinates with a solvated box rather than
truncated octahedron?
Many thanks in advance,
Ben
On 16 May 2014 15:45, Brian Radak <radak004.umn.edu> wrote:
> Without accounting for PBCs RDFs are definitely sensitive to wrapping if
> the reference sites are near the boundary. This sounds like it might be the
> case for you if you don't just have a single macromolecule in the center of
> a water box. Cpptraj can definitely solve this problem by handling PBCs
> correctly when doing the RDF calculation (see the "radial" function in the
> AmberTools manual). The RDF utility in VMD, on the other hand, can only
> handle orthorhombic conditions (to the best of my knowledge), although it
> will not tell you that it has messed up the coordinates.
>
> Regards,
> Brian
>
> P.S. There is no real gain in converting an ASCII trajectory to NetCDF
> format after the fact except to compress the data and speed up file
> reading; all of the precision is already lost. I would recommend ALWAYS
> using ioutfm = 1 and ntxo = 2 whenever running AMBER.
>
>
> On Fri, May 16, 2014 at 10:29 AM, Ben Ahmady <ahmady.ben.gmail.com> wrote:
>
> > Dear AMBER Users & Developers,
> >
> > I've developed an SDS micelle trajectory in AMBER of 60 surfactants, and
> > I've taken a window of the last 4ns of a ~25ns NPT run with iwrap=0,
> using
> > ptraj, and put it into a NETCDF-formatted coordinate file, using the
> > commands:
> >
> > """
> > trajin last4ns.crd
> > center :1-60
> > image familiar
> > trajout centre.crd netcdf
> > """
> >
> > I've then generated an RDF with the following command:
> >
> > """
> > radial centre 0.1 10 :1-60.S39 :61-120 :SDS.S39 density 0.00088 noimage
> > """
> >
> > This gives me something sensible looking, with coordination shells I'd
> > expect from previous work, but I've gotten very confused about how I
> should
> > go about "counting" the number of ions within distances corresponding to
> > the coordination shell boundaries. The only way I can think of is to use
> > VMD commands of the order:
> >
> > """
> > set sel [atomselect top "all name 'Na+' and within X of name 'S39'"]
> > $sel num
> > """
> >
> > ... but I'm not sure if I should be using wrapped coordinates, or an
> > average structure (via ptraj's "average" routine), or whether I should be
> > including imaging, and so on. I get different results for different
> > combinations I've tried — so to put it another way I don't know which one
> > is actually giving me the "right" answer.
> >
> > Apologies if this would be better suited to the VMD mailing list, but I
> > thought it might have more to do with the way I've generated my
> > coordinates, implying I actually need help with AMBER/ptraj. In any case,
> > any assistance would be greatly appreciated.
> >
> >
> > Best regards,
> >
> > Ben Ahmady
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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>
--
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 Fri May 16 2014 - 10:00:03 PDT
