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

Adarsh V. K. adarsh_p130085bt at nitc.ac.in
Mon Apr 23 09:21:28 CEST 2018

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
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
, 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.

*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

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