> I'm using cpptraj to analyze a set of trajectories run on Anton. My
> previous pipeline for getting them into cpptraj was to use VMD to convert
> them from Anton's binary format to Amber's text coordinate format (what VMD
> calls 'crd'), and then use cpptraj to convert them to netcdf (which VMD
> cannot write to directly). VMD's output is as follows:
An alternative to .trr is DCD (CHARMM) format; to avoid blowing memory
with vmd conversion, I did the conversion in chunks... Then you can load
up CPPTRAJ or ptraj using a corresponding PDB file in place of the
prmtop/psf.
--tec3
#!/bin/csh
/uufs/chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd -dispdev text sys0.cms <<EOF
animate read dtr workdir/run.stk beg 0 end 20000 waitfor all 0
animate write dcd GAAC3.dcd.1 beg 1 0
quit
EOF
/uufs/chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd -dispdev text sys0.cms <<EOF
animate read dtr workdir/run.stk beg 20001 end 40000 waitfor all 0
animate write dcd GAAC3.dcd.2 beg 1 0
quit
EOF
/uufs/chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd -dispdev text sys0.cms <<EOF
animate read dtr workdir/run.stk beg 40001 end 60000 waitfor all 0
animate write dcd GAAC3.dcd.3 beg 1 0
quit
EOF
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Received on Thu Jul 02 2015 - 13:00:03 PDT
