GROMACS version: 2023
GROMACS modification: No
Hello, i am running the specific tutorial step by step but during the energy minimization with the tutorial .mdo file and the following command i am receiving that error:
Command line:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol2.top -r system_inflated.gro -o system_inflated_em.tpr
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file minim_inflategro.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -862724
WARNING 1 [file ffnonbonded.itp, line 3126]:
Bondtype LJ-14 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
old: 0.00261735 2.63413e-06 0.00261735 2.63413e-06
new: OW OW 1 3.31400e-04 3.36000e-07
Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘DPPC’
WARNING 2 [file topol2.top, line 928]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding. Further information is available at
GROMACS can not reproduce properties with the GROMOS force fields - Redmine #2884 (#2884) · Issues · GROMACS / GROMACS · GitLab, and a longer
explanation of our decision to remove physically incorrect algorithms can
be found at On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .
NOTE 2 [file topol2.top, line 928]:
System has non-zero total charge: 4.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
ERROR 1 [file topol2.top, line 928]:
Empty diagonal for a 3-dimensional periodic box
ERROR 2 [file topol2.top, line 928]:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.
There were 2 NOTEs
There were 2 WARNINGs
Program: gmx grompp, version 2023
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2198)
Fatal error:
There were 2 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
An other more common case is this:
Command line:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol2.top -r system_inflated.gro -o system_inflated_em.tpr
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file minim_inflategro.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -62915081
WARNING 1 [file ffnonbonded.itp, line 3126]:
Bondtype LJ-14 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
old: 0.00261735 2.63413e-06 0.00261735 2.63413e-06
new: OW OW 1 3.31400e-04 3.36000e-07
Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘DPPC’
WARNING 2 [file topol2.top, line 928]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding. Further information is available at
GROMACS can not reproduce properties with the GROMOS force fields - Redmine #2884 (#2884) · Issues · GROMACS / GROMACS · GitLab, and a longer
explanation of our decision to remove physically incorrect algorithms can
be found at On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .
NOTE 2 [file topol2.top, line 928]:
System has non-zero total charge: 4.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
Program: gmx grompp, version 2023
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 706)
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6538)
does not match topology (topol2.top, 6438)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
But i edit the top file and then i get the first error
Does anybody know what is wrong?