[gmx-users] Problem in Free Energy Calculations

[shagun krishna]

Hi Justin...

I am following your Free Energy Calculations: Methane in Water tutorial. I
am running it with the example files only. However I am little confused
about some line written in it. It is written there :

You should probably change the values of $FREE_ENERGY and $MDP, otherwise
they likely won't work. Please also note that the write_sh.pl script writes
trailing zeroes in the job_*.sh files that you will need to remove for the
scripts to actually work. For instance, in job_0.sh, you will find:

LAMBDA = 0.00

However, the corresponding .mdp files will be named em_steep_0.mdp,
em_l-bfgs_0.mdp, etc, not em_steep_0.00.mdp, em_l-bfgs_0.00.mdp, etc. The
same will be true for λ = 0.1, 0.2, 0.3, and so on. Remove all trailing
zeroes from the values assigned to LAMBDA.

What I am doing is to open the job_0.sh, job_0.1.sh, job_0.2.sh......
job_0.9.sh files and removing the trailing zeros making it LAMBDA = 0,
LAMBDA = 0.1....LAMBDA = 0.9. When I am running the job.sh script I am
getting a series of errors for every step:

-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524

Can not open file:
nvt0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524

Can not open file:
npt0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/futil.c, line: 593

File input/output error:
/home/cbb/justin/Free_Energy/MDP/Production_MD/md_0.mdp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524

Can not open file:
md0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-----------------------------------------------------
"Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw)

Production MD complete.
Ending. Job completed for lambda = 0

More over I could not understand how to change the values of $FREE_ENERGY
and $MDP. I guess that probably this may be a reason for above errors. In
free energy folder, a folder named Lambda_0 is created and inside it five
folders are generated. But log file present in all of them have error of
similar type:


-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524

Can not open file:
min0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw)


Please guide me where I am wrong and how to run this tutorial successfully.

Regards,

Shagun Krishna