[gmx-users] About script for free energy calculation

[Mark Abraham]

On Tue, Aug 27, 2013 at 7:05 PM, vidhya sankar <scvsankar_agr at yahoo.com> wrote:
> 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)

Don't. Your root privileges have just been revoked. :-) Learn to
source GMXRC like the installation instructions say.

Mark

> 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
>
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