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

[lazaro monteserin]

Dear Lemkul

Thank you very much for the recommendation.

I tried each step but separate and you were right I was missing the .gro in
my directory.

Now the script should work. But I am still unsure of how to declare the
location of my file in the environmental variable $FREE_ENERGY and $MDP. Do
you have any suggestions.

The location of my file is /home/Lazaro/tutorial_gromacs

Kindly,

Lazaro

El jue., 16 de abr. de 2020 a la(s) 13:01, Justin Lemkul (jalemkul at vt.edu)
escribió:

>
>
> 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
>
> --
> ==================================================
>
> 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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