Jason, thanks!
Some new questions:
1) Does it possible to re-start previously manually terminated simulation
(using restr file) and write trajectory in the existing .crdbox file
preventing creation of new one for restarting run?
2)More specified question: I need to calculate number of water molecules
which are within selected cutoff distance or radius to the selected protein
residue along my trajectory. I've found some VMD scripts for this task but
it has shown wrong (mainly overestimated) results (this time I've analyzed
dcd trajectory created from the amber's crdbox). I'll be very thankful if
someone also have faced with the same problem and has some script for such
task.
TFH,
James
2014-05-22 17:22 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> 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 Sun May 25 2014 - 04:00:02 PDT
