c-shell into NAMD configuration file

From: Ioana Cozmuta (ioana73_at_gmail.com)
Date: Mon Jun 13 2005 - 02:02:48 CDT

 I am trying to set in the NAMD configuration file the name of the directory
where the output files generated by NAMD will be written. However the exec
command does not seem to be recognized by NAMD.
Any suggestion?
 I am including below the test configuration file.
 Thank you,
#Configuration file for NAMD, NVT run trying to heat up a water box
#from 0K to 300K
exec sh -c {setenv DIR `date +%m_%d_%H_%M_%y`}
exec sh -c {mkdir $DIR}

exec sh -c {echo $DIR}
set inputname test1
set outputname test2

# initial config
exclude scaled1-4
1-4scaling 0.8333 #=1/1.2 from Amber
scnb 2.0 #this is for the van der waals
amber on
parmfile ../test.prmtop
coordinates ../test/$inputname.coor
velocities ../test/$inputname.vel
extendedSystem ../test/$inputname.xsc

restartfreq 1000
outputEnergies 50
outputTiming 1000
xstFreq 1000
dcdFreq 50
outputname ./$DIR/$outputname.out
restartname ./$DIR/$outputname.restrt
binaryrestart no
binaryoutput no
DCDfile ./$DIR/$outputname.dcd
COMmotion no

switching on
switchdist 8
cutoff 9.5
pairlistdist 10.0

#Amber uses rigid water and SHAKE H-bonds.
rigidBonds all

timestep 1

nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20

fixedAtoms on
fixedAtomsForces on
fixedAtomsFile ../fix.pdb
fixedAtomsCol B

# full electrostatics
Pme on
PmeGridSizeX 32
PmeGridSizeY 32
PmeGridSizeZ 32

# protocol params
numsteps 20000

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:50 CST