Variable Not getting recognized in shell script

Question

I use the following shell script to run a simulation on my cluster.

  #PBS -N 0.05_0.05_m_1_200k
  #PBS -l nodes=1:ppn=1,pmem=1000mb
  #PBS -S /bin/bash
  #$ -m n
  #$ -j oe


  FOLDER= 0.57

  WDIR=/home/vikas/ala_1_free_energy/membrane_200k/restraint_decoupling_pullinit_$FOLDER

  cd /home/vikas/ala_1_free_energy/membrane_200k/restraint_decoupling_pullinit_$FOLDER

  LAMBDA= 0.05

 /home/durba/gmx455/bin/mdrun -np 1 -deffnm md0.05 -v

 ############################

Now my problem is that my script doesn't recognize variable FOLDER and throws an error

     couldn't find md0.05.tpr

which exist in the folder. If I write 0.57 at the place of $folder,It works fine, which makes me feel that it's not recognizing the variable FOLDER. LAMBDA is recognized perfectly in both of the cases.If somebody can help me here, I will be grateful.

user4832408 · Accepted Answer · 2015-10-06 12:14:39Z

2

There should not be a space between the = and the value you wish to assign to the variables:

FOLDER="0.57"

WDIR="/home/vikas/ala_1_free_energy/membrane_200k/restraint_decoupling_pullinit_$FOLDER"

cd "/home/vikas/ala_1_free_energy/membrane_200k/restraint_decoupling_pullinit_$FOLDER"

LAMBDA="0.05"

/home/durba/gmx455/bin/mdrun -np 1 -deffnm md0.05 -v

############################

All of the double quotes "" I added are not strictly necessary for this example, however it is good practice to get into using them.

answered Oct 6, 2015 at 12:14

user4832408

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