GROMACS version:2021-rc1
GROMACS modification: No
How can I get over this problem ?
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘optimize_fft’
Ignoring obsolete mdp entry ‘ns_type’
Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’
Setting the LD random seed to -1258291201
Generated 2145 of the 2145 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2145 of the 2145 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_E’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_I’
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…
Excluding 1 bonded neighbours molecule type ‘CL’
turning H bonds into constraints…
Pull group 1 ‘Chain_E’ has 3564 atoms
Pull group 2 ‘Chain_I’ has 861 atoms
Number of degrees of freedom in T-Coupling group Protein is 9552.64
Number of degrees of freedom in T-Coupling group non-Protein is 70181.36
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.433 nm, buffer size 0.033 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
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 56x40x100, spacing 0.117 0.109 0.119
ERROR 1 [file md_pull.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 1 is larger than that
and does not have a specific atom selected as reference atom.
Pull group natoms pbc atom distance at start reference at t=0
1 3564 1782
2 861 3389 0.165 nm 0.165 nm
Estimate for the relative computational load of the PME mesh part: 0.13
This run will generate roughly 319 Mb of data
Program: gmx grompp, version 2021-rc1-UNCHECKED
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2382)