GROMACS version: 2022
GROMACS modification: No
I’m working on the second tutorial of build a membrane. After the step of packing the lipids around the protein (where you use the comand $ perl inflategro.pl system_inflated_em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat) the work is done perfectly but the next step the programm using the bash script the programm print the error below:
root@LAPTOP-HFHE2FMF:/home/usr/gromacs-2022.3/Tutorials/Membrana# bash run_inflategro.sh
:-) GROMACS - gmx grompp, 2022.3 (-:
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/usr/gromacs-2022.3/Tutorials/Membrana
Command line:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr -maxwarn 3
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 2146942191
WARNING 1 [file ffnonbonded.itp, line 3123]:
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 topol.top, line 929]:
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.
NOTE 2 [file topol.top, line 929]:
System has non-zero total charge: 4.000000
Total charge should normally be an integer. See
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 17 Protein residues
There are: 126 Other residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 19311.00
NOTE 3 [file minim_inflategro.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.
NOTE 4 [file minim_inflategro.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 1 Mb of data
There were 4 notes
There were 2 warnings
GROMACS reminds you: “… yet the [economic] profession continued to churn out purely theoretical results without even knowing what facts needed to be explained.” (Thomas Piketty)
:-) GROMACS - gmx mdrun, 2022.3 (-:
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/usr/gromacs-2022.3/Tutorials/Membrana
Command line:
gmx mdrun -deffnm system_inflated_em
Reading file system_inflated_em.tpr, VERSION 2022.3 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 75 steps
Potential Energy = -9.5797906e+04
Maximum force = 8.5091754e+02 on atom 78
Norm of force = 6.5768953e+01
GROMACS reminds you: “Programming today is a race between software engineers striving to build bigger and better idiot-proof programs, and the universe trying to build bigger and better idiots. So far, the universe is winning.” (Rick Cook)
:-) GROMACS - gmx trjconv, 2022.3 (-:
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/usr/gromacs-2022.3/Tutorials/Membrana
Command line:
gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro -pbc mol
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write gro: Coordinate file in Gromos-87 format
Reading file system_inflated_em.tpr, VERSION 2022.3 (single precision)
Reading file system_inflated_em.tpr, VERSION 2022.3 (single precision)
Select group for output
Group 0 ( System) has 6438 elements
Group 1 ( Protein) has 138 elements
Group 2 ( Protein-H) has 109 elements
Group 3 ( C-alpha) has 16 elements
Group 4 ( Backbone) has 48 elements
Group 5 ( MainChain) has 64 elements
Group 6 ( MainChain+Cb) has 78 elements
Group 7 ( MainChain+H) has 81 elements
Group 8 ( SideChain) has 57 elements
Group 9 ( SideChain-H) has 45 elements
Group 10 ( Prot-Masses) has 138 elements
Group 11 ( non-Protein) has 6300 elements
Group 12 ( Other) has 6300 elements
Group 13 ( DPPC) has 6300 elements
Select a group: Selected 0: ‘System’
Reading frames from gro file ‘frame t= 1.000’, 6438 atoms.
Reading frame 0 time 1.000
Precision of system_inflated_em.gro is 0.001 (nm)
Last frame 0 time 1.000
→ frame 0 time 1.000
Last written: frame 0 time 1.000
GROMACS reminds you: “Programming today is a race between software engineers striving to build bigger and better idiot-proof programs, and the universe trying to build bigger and better idiots. So far, the universe is winning.” (Rick Cook)
########################################
RUNNING SHRINKING ITERATION 1…
########################################
Reading…
Scaling lipids…
There are 126 lipids…
with 50 atoms per lipid…
Determining upper and lower leaflet…
63 lipids in the upper…
63 lipids in the lower leaflet
Centering protein…
Writing scaled bilayer & centered protein…
Calculating Area per lipid…
Protein X-min/max: 122 136
Protein Y-min/max: 122 135
X-range: 14 A Y-range: 13 A
Building 14 X 13 2D grid on protein coordinates…
Calculating area occupied by protein…
full TMD…
upper TMD…
lower TMD…
Area per protein: 2 nm^2
Area per lipid: 9.44753187580952 nm^2
Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 9.45150012977778 nm^2
Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 9.44753187580952 nm^2
Writing Area per lipid…
Done!
:-) GROMACS - gmx grompp, 2022.3 (-:
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/usr/gromacs-2022.3/Tutorials/Membrana
Command line:
Command line:
gmx grompp -f minim_inflategro.mdp -c system_shrink1.gro -r system_shrink1.gro -p topol.top -o system_shrink1_em.tpr - maxwarn 3
Program: gmx grompp, version 2022.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -o
Too many values
In command-line option -o
Too many values
In command-line option -o
Too many values
For more information and tips for troubleshooting, please check the GROMACS
website at
Please, someone can help me
Thank you in advance