[gmx-users] Gromacs 2018.1 Errors while working with tutorial; gromacs.org_gmx-users Digest, Vol 168, Issue 108

[Adarsh V. K.]

Dear Justin A. Lemkul,

 Would you please suggest how the modifications can be applied?

gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr (Tutorial
Lysozyme in Water)

I got following errors while issuing above command.

Ignoring obsolete mdp entry 'title'
Setting the LD random seed to 935164351
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to -426374842
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

-------------------------------------------------------
Program:     gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
>From GROMACS-2018, you need to specify the position restraint coordinate
files
explicitly to avoid mistakes, although you can still use the same file as
you
specify for the -c option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-----------------------------------------------

> Message: 3
> Date: Mon, 23 Apr 2018 08:19:01 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
>
> 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/gm
> x-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
>
>