[gmx-users] Gromacs 2018.1 Errors while working with tutorial

[Justin Lemkul]

On 4/23/18 3:21 AM, Adarsh V. K. wrote:
> Dear Gromacs Users,
>
> I have installed Gromacs 2018.1 in a system with Ubuntu 16.04, cuda 8 and
> GTX1080Ti. The compilation part regressiontests and installation of Gromacs
> 2018.1 was successful with out any errors. Before doing actual experiments
> with new version, I thought of working with GROMACS Tutorial
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/>
> (*Justin
> A. Lemkul, Ph.D.**, Department of Pharmaceutical Sciences,University of
> Maryland, Baltimore*). But while working with examples from tutorial,
> returns a number of errors..! . For example  Tutorial 1: Lysozyme in Water
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html>
> , the fourth step itself giving errors, But same example is working perfect
> with Gromcs 5.1.4. Can you please suggest any modifications? Is it a
> problem with .mdp file?. Is there any new tutorial for Gromacs 2018.1?
>
> How to uninstall Gromacs 2018.1 and reinstall Gromacs 5.1.5; Just deleting
> /usr/local/gromacs is sufficient? (Ubuntu 16.04) before re-installing.
> --------------------------------
> gromacs 2018.1 Error detail (Tutorial)
> Tutorial 1: Lysozyme in Water
>
> *Command line:*
>    gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
>
> NOTE 1 [file ions.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20.
>
> NOTE 2 [file topol.top, line 18409]:
>    System has non-zero total charge: 8.000000
>    Total charge should normally be an integer.
>
> WARNING 1 [file topol.top, line 18409]:
>    You are using Ewald electrostatics in a system with net charge. This can
>    lead to severe artifacts, such as ions moving into regions with low
>    dielectric, due to the uniform background charge.
>
> Fatal error:
> Too many warnings (1).
> If you are sure all warnings are harmless, use the -maxwarn option.

In this case, -maxwarn is safe because the .tpr file is not actually 
being used for dynamics.

Alternatively, remove PME from the .mdp file (replace with a simple 
cutoff) again because the .tpr is not being used for anything terribly 
important.

-Justin

> *Command line:*
> gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname
> CL -nn 8
>
> Error in user input:
> Invalid command-line options
> In command-line option -s
> File 'ions.tpr' does not exist or is not accessible.
> The file could not be opened.
> Reason: No such file or directory

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

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