Hi,
Hmm...I'm not sure how NAMD stores unit cell info in the DCD
trajectory. According to CHARMM, since version 22 the symmetric shape
matrix is stored instead of unit cell parameters. The weird angle
you're getting for truncated octahedron makes me suspect that the unit
cell information in your trajectory is actually unit cell parameters.
This can be easily tested if you have a version of cpptraj laying
around < 16.16 - prior to this cpptraj didn't understand the shape
matrix info output by CHARMM. If this is indeed the case I'll have to
update cpptraj so it can figure out (or be told) what kind of unit
cell parameters are in a DCD file.
-Dan
On Tue, Nov 29, 2016 at 1:56 PM, Brian Radak
<brian.radak.accts.gmail.com> wrote:
> I just downloaded AmberTools16 today, Cpptraj V16.16.
>
> There are probably a number of places weird things could happen. Maybe the
> following observations are relevant:
>
> 1) the CHARMM PSF format does not include *any* box information
> 2) the extended system (xsc) file that I used in my simulation weirdly has
> all zeros for the angles (I guess because NAMD uses (can use?) a full
> vector specification instead?)
> 3) I have little idea as to how the DCD trajectories store box information
> 4) this was a constant volume simulation
>
> On Tue, Nov 29, 2016 at 12:48 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> What version of cpptraj are you using? Something is clearly off since
>> those are definitely not angles for a truncated octahedron cell.
>>
>> -Dan
>>
>> On Tue, Nov 29, 2016 at 1:24 PM, Brian Radak
>> <brian.radak.accts.gmail.com> wrote:
>> > I have a NAMD DCD trajectory and PSF generated with triclinic boundary
>> > conditions corresponding to a truncated octahedron, but am having trouble
>> > getting the trajectory into "familiar" form via cpptraj (which is
>> > apparently the only utility around that can handle this procedure?).
>> >
>> > I did the following:
>> >>> cpptraj -p my.psf -y my.dcd
>> >
>> > Which gave the following helpful warning:
>> >
>> > Warning: Trajectory box type is 'Non-orthogonal' but topology box type is
>> > 'None'.
>> > Warning: Setting topology box information from trajectory.
>> >
>> > Then
>> >>> autoimage
>> >>> trajout my.rewrap.dcd
>> >>> go
>> >
>> > However, loading the output dcd into VMD instead shows an orthorhombic
>> cell
>> > with missing slabs at a diagonal. I checked that the
>> a/b/c/alpha/beta/gamma
>> > were what I thought they should be:
>> >>> parmbox
>> > Box: 'Non-orthogonal' XYZ= { 83.503 83.503 83.503 } ABG= {
>> > 89.54 89.54 90.46 }
>> >
>> > Which did not seem right, so I tried again with:
>> >>> parmbox truncoct 83.503
>> >
>> > but this has the same result. I saw indications in the list archive that
>> > similar things have been encountered before, but no obvious solutions.
>> Any
>> > ideas?
>> >
>> > Thanks,
>> > Brian
>> >
>> > --
>> > Brian Radak
>> > Postdoctoral Appointee
>> > Leadership Computing Facility
>> > Argonne National Laboratory
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak.anl.gov
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Nov 29 2016 - 11:30:02 PST
