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
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Received on Fri May 16 2014 - 08:00:02 PDT
