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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Received on Fri May 16 2014 - 08:00:03 PDT
