[gmx-users] About script for free energy calculation

[vidhya sankar]

Dear Justin thank you for your Previous reply
      I am following your methane/water free energy tutorial
I have Generated All .mdp files wiht Different LAMBDA value But When I Run job using Your Job.sh  script
 in usr/local/gromacs4.6.2/bin I have Received the Following error  ( I ma running this script by keepig in BIN directory)

root at vidhyasankar-desktop:/usr/local/gromacs4.6.1/bin# ./job.sh  ( the error is as follows)


Free energy home directory set to /usr/local/gromacs4.6.1/bin/Free_Energy
.mdp files are stored in /usr/local/gromacs4.6.1/bin/Free_Energy/MDP
Starting minimization for lambda = 0...
./job.sh: line 28: grompp_d: command not found
./job.sh: line 30: mdrun_d: command not found
./job.sh: line 41: grompp_d: command not found
./job.sh: line 45: mdrun_d: command not found
Minimization complete.
Starting constant volume equilibration...
./job.sh: line 60: grompp_d: command not found
./job.sh: line 62: mdrun_d: command not found
Constant volume equilibration complete.
Starting constant pressure equilibration...
./job.sh: line 77: grompp_d: command not found
./job.sh: line 79: mdrun_d: command not found
Constant pressure equilibration complete.
Starting production MD simulation...
./job.sh: line 93: grompp_d: command not found
./job.sh: line 95: mdrun_d: command not found
Production MD complete.
Ending. Job completed for lambda = 0

How to Solve it 

Thanks InAdvance