On Thu, 2014-05-22 at 16:52 +0400, James Starlight wrote:
> When I've tried to convert my amber 100ns trajectory to dxd using cpptraj
> it took about 1 hour :) Does catDCD or any other terminal utilities can do
> such tasks?
This sounds like a filesystem issue. You can also look into mdconvert
(part of the MDTraj Python suite) available here:
http://mdtraj.org/latest/
Or you can use VMD (which uses catDCD, I believe). I believe the DCD
reading/writing code from MDTraj uses the VMD plugin (which, like I
said, is the same as catDCD, I think). When I tested cpptraj and
mdconvert on my machine with a 22K atom system with a 6.9 GB trajectory
(100 ns), cpptraj took 53 seconds and mdconvert took 51 seconds.
>
> By the way also I have a question about proper loading of the trajectories
> to the VMD
>
> e.g using
> vmd ionized.prmtop md.mdcrd
>
> VMD recognize this trajectory as without PB box. Does it possible to fix it
> providing some flag to VMD?
vmd -parm7 ionized.prmtop -crdbox md.mdcrd
Other helpful flags for VMD:
-netcdf <netcdf file> (.nc)
-crd <amber mdcrd without box> (.mdcrd, .crd)
-rst7 <amber inpcrd or restart file> (.rst7)
In parentheses are the filename extensions that are autodetected (and
therefore don't need the flag)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 22 2014 - 06:30:02 PDT
