below is the code and the output.
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, 2022.4 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/aqsakhalid/Documents/MD_simulation/MSP_simulation
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).
For isotropic scaling we would recommend the C-rescale barostat that also
ensures fast relaxation without oscillations, and for anisotropic scaling
you likely want to use the Parrinello-Rahman barostat.
Setting the LD random seed to -147064889
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘LIG7’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘NA’
turning H bonds into constraints…
Cleaning up constraints and constant bonded interactions with virtual sites
The center of mass of the position restraint coord’s is 5.937 6.640 2.194
The center of mass of the position restraint coord’s is 5.937 6.640 2.194
Number of degrees of freedom in T-Coupling group Protein_LIG7 is 8699.55
Number of degrees of freedom in T-Coupling group Water_and_ions is 48825.45
The largest distance between excluded atoms is 0.850 nm
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
NOTE 1 [file npt.mdp]:
There are 2 non-linear virtual site constructions. Their contribution to
the energy error is approximated. In most cases this does not affect the
error significantly.
Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.092 nm
Set rlist, assuming 4x4 atom pair-list, to 1.219 nm, buffer size 0.019 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
NOTE 2 [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 48x48x48, spacing 0.154 0.154 0.154
Estimate for the relative computational load of the PME mesh part: 0.15
This run will generate roughly 16 Mb of data
There were 2 notes
There was 1 warning
Program: gmx grompp, version 2022.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2661)
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.