GROMACS version:2021.3
GROMACS modification: Yes/No
Here post your question : How to rectify this error and
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file ions.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 54285822
ERROR 1 [file jz4.prm, line 61]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 2 [file jz4.prm, line 158]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 3 [file jz4.prm, line 159]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 4 [file jz4.prm, line 160]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117519 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘JZ4’
NOTE 2 [file topol.top, line 25056]:
System has non-zero total charge: -6.000000
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.
Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 669)
Fatal error:
number of coordinates in coordinate file (solv.gro, 197725)
does not match topology (topol.top, 2731)
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs.
There is a lot of difference between coordinate numbers how to rectify it.
Thanking you,
Shravan Kumar G