[gmx-users] Problem in Free Energy Calculations

[Justin Lemkul]

On 12/31/15 1:21 AM, shagun krishna wrote:
> 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
> -------------------------------------------------------

If you are using version 4.6.5, you must be using some old version of the 
tutorial (which used different nomenclature for the job files).  Use the latest 
GROMACS version 5.1.1 and use the current tutorial.  There are no such issues 
that I am aware of with it.  If you are trying to run the current tutorial with 
old software, that explains why your .tpr files aren't being created.  The 
software is incompatible with the tutorial.

 From the home page of the tutorial:

"This tutorial requires a minimum GROMACS version of 5.0. Due to major changes 
in the way the free energy options are handled, any version prior to 5.0 will 
not work."

-Justin

> -------------------------------------------------------
> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================