[gmx-users] about problem running script for Gibbs free energy simulation

[Justin Lemkul]

On 4/16/20 11:48 AM, lazaro monteserin wrote:
> Dear Gromacs users,
>
> I have been trying to do the tutorial title: "Free Energy Calculations:
> Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my
> paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I have
> problems and I get the following error:
>
> Program:     gmx mdrun, version 2020.1
> Source file: src/gromacs/options/options.cpp (line 179)
> Function:    void gmx::internal::OptionSectionImpl::finish()
> Error in user input:
> Invalid input values
>    In option s
>      Required option was not provided, and the default file 'topol' does not
>      exist or is not accessible.
>      The following extensions were tried to complete the file name:
>        .tpr
>
> My path for the .mdp files would be: "/home/Lazaro/tutorial_gromacs" for
> example.
>
> Any help?

grompp is failing and not creating the .tpr files you need, so mdrun 
tries to rely on default file names, which also don't exist. Run the 
commands interactively, one by one, to find the error. When you've 
resolved that, you can use the script's automated approach.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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