...
Note that this requires runavg.awk, and density calculations are correct only for simulation cell types where Volume = a*b*c. Run with options "--usage" or "--help" for more details:
...
Usage:
...
basic_analysis.sh
...
--name
...
SIMNAME
...
[
...
--logfile
...
FILE
...
]
...
[
...
--psf
...
PSFFILE
...
]
...
[
...
--outputdir
...
ODR
...
]
...
[
...
--dcdfreq
...
N
...
]
...
[
...
--rmsdsel
...
SELTEXT
...
]
...
Performs
...
simple
...
analysis
...
tasks
...
for
...
simulation
...
without
...
output
...
SIMNAME.
...
OPTIONS:
...
--logfile
...
FILE
...
:
...
Use
...
FILE
...
as
...
NAMD
...
log
...
file.
...
Default
...
value
...
is
...
SIMNAME.log
...
--psf
...
PSFFILE
...
:
...
Use
...
PSFFILE
...
(either
...
CHARMM
...
or
...
AMBER
...
format)
...
as
...
system
...
topology
...
file.
...
Should
...
have
...
.psf
...
or
...
.parm7
...
extension
...
for
...
filetype
...
recognition
...
by
...
VMD.
...
Default
...
value:
...
SIMNAME.psf
...
--outputdir
...
ODR:
...
Write
...
analysis
...
output
...
to
...
directory
...
ODR.
...
Figures
...
will
...
go
...
to
...
ODR/figures/.
...
Default
...
value:
...
$(dirname
...
SIMNAME)/analysis_output/
...
--dcdfreq
...
N
...
:
...
Frequency
...
at
...
which
...
frames
...
were
...
written
...
to
...
DCD
...
file
...
SIMNAME.dcd.
...
Default
...
100.
...
--rmsdsel
...
SELTXT:
...
VMD
...
selection
...
text
...
for
...
RMSD
...
calculation.
...
Must
...
be
...
enclosed
...
in
...
quotes.
...
Default
...
value:
...
"all".
...
Sample scripts for basic tasks in CHARMM
...