:-) GROMACS - gmx grompp, 2022-conda_forge (-: Executable: /usr/local/tools/_conda/envs/__gromacs@2022/bin.AVX2_256/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2022 Working dir: /data/jwd02f/main/075/566/75566343/working Command line: gmx grompp -f ./md.mdp -c ./inp.gro -t ./inp.cpt -p ./top_input.top -o outp.tpr -maxwarn 0 Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'ns_type' Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file top_input.top, line 31059]: The bond in molecule-type Protein_chain_A between atoms 44 OG1 and 45 HG1 has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group Protein is 9839.47 Number of degrees of freedom in T-Coupling group non-Protein is 46176.53 Last frame -1 time 50.000 There was 1 note GROMACS reminds you: "Drugs are Bad, mmokay" (South Park) Setting the LD random seed to -1628439813 Generated 3003 of the 3003 non-bonded parameter combinations Generated 3003 of the 3003 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'base' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Analysing residue names: There are: 208 Protein residues There are: 1 Other residues There are: 7683 Water residues There are: 6 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... The largest distance between excluded atoms is 0.424 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.011 nm, buffer size 0.011 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 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 Using frame at t = 50 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.154 0.154 0.153 Estimate for the relative computational load of the PME mesh part: 0.22 This run will generate roughly 736 Mb of data :-) GROMACS - gmx mdrun, 2022-conda_forge (-: Executable: /usr/local/tools/_conda/envs/__gromacs@2022/bin.AVX2_256/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2022 Working dir: /data/jwd02f/main/075/566/75566343/working Command line: gmx mdrun -nt 8 -deffnm outp Reading file outp.tpr, VERSION 2022-conda_forge (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1.117 Using 1 MPI thread Using 8 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'HEAT SHOCK PROTEIN HSP 90-ALPHA' 1000000 steps, 1000.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 35719.342 4464.922 800.0 1h14:24 (ns/day) (hour/ns) Performance: 19.351 1.240 GROMACS reminds you: "Disturb the Peace of a John Q Citizen" (Urban Dance Squad) title = OPLS Lysozyme MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 1000000 ; 2 * 500000 = 1000 ps (1 ns) dt = 0.001 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 10.0 ps nstvout = 1000 ; save velocities every 10.0 ps nstenergy = 1000 ; save energies every 10.0 ps nstlog = 1000 ; update log file every 10.0 ps nstxout-compressed = 1000 ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System ; group(s) to write to the compressed trajectory file ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; Short-range electrostatic cut-off rlist = 1.0 ; Cut-off distance for the short-range neighbor list. rvdw = 1.0 ; Short-range Van der Waals cut-off ; Electrostatics coulombtype = PME ; method for electrostatics calculations e.g. PME pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is OFF pcoupl = no ; no pressure coupling in NVT