[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
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.
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
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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