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

[Mark Abraham]

Hi,

Position restraints require you to say to which positions you are
restraining. grompp now requires you to be explicit about that, rather than
assuming you want the positions contained in the -c file, because people
found that mysterious and wondered which coordinates they were restraining
do. So if you want the old behaviour, use grompp -c some.gro -r some.gro

Mark

On Thu, Apr 26, 2018 at 7:20 AM Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
wrote:

> 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
> >
> >
> --
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