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gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr
:-) GROMACS - gmx grompp, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /mnt/c/sm
Command line:
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’
WARNING 1 [file npt.mdp]:
The Berendsen barostat does not generate any strictly correct ensemble,
and should not be used for new production simulations (in our opinion).
We recommend using the C-rescale barostat instead.
Setting the LD random seed to 2075302583
Generated 22578 of the 22578 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 19461 of the 22578 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_D’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Ligand’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘NA’
turning H bonds into constraints…
The center of mass of the position restraint coord’s is 13.011 13.020 6.139
The center of mass of the position restraint coord’s is 13.011 13.020 6.139
Number of degrees of freedom in T-Coupling group Protein_LIG is 71565.71
Number of degrees of freedom in T-Coupling group Water_and_ions is 673953.31
The largest distance between excluded atoms is 0.441 nm between atom 16755 and 16763
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.294 nm, buffer size 0.094 nm
Set rlist, assuming 4x4 atom pair-list, to 1.222 nm, buffer size 0.022 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
NOTE 1 [file npt.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.
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame -1 time 100.000
Using frame at t = 100 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 112x112x112, spacing 0.155 0.155 0.155
Estimate for the relative computational load of the PME mesh part: 0.11
This run will generate roughly 204 Mb of data
There was 1 NOTE
There was 1 WARNING
Program: gmx grompp, version 2023.3-Ubuntu_2023.3_1ubuntu3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2691)
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.