Apologies for double-post: just wanted to confirm that I fixed it by using
"density 0.00262" (from 0.6022/10*23 for sodium) instead of "volume".
Imaging being on or off (i.e. presence or lack of "noimage" switch) no
longer seems to make any difference.
Thanks again very much for all the help.
Ben
On 18 May 2014 20:43, Ben Ahmady <ahmady.ben.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> 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/
>
>
>
>
>
--
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 Mon May 19 2014 - 02:30:04 PDT
