[gmx-users] Problem in Free Energy Calculations

[shagun krishna]

Hii Justin,

I am using the old version of gromacs i.e 4.6.5 and the tutorial that I am
following is also compatible with the same version. Then too I am getting
the problem.

One more thing if I got the energy for the ligand and the protein how would
I combine them to single .edr file since gmx lie program uses a single file
such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr
<http://manual.gromacs.org/online/edr.html> file. and How I will get the
values of  Elj, Eqq, Clj, Cqq.

Thanks and regards,

shagun

On Thu, Dec 31, 2015 at 7:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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