:-) GROMACS - gmx solvate, 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/075/528/75528529/working Command line: gmx solvate -cp ./gro_input.gro -cs spc216.gro -o solv.gro -p ./top_input.top Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 4x4x4 boxes Solvent box contains 30576 atoms in 10192 residues Removed 4338 solvent atoms due to solvent-solvent overlap Removed 3171 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 7689 residues Generated solvent containing 23067 atoms in 7689 residues Writing generated configuration to solv.gro Output configuration contains 26368 atoms in 7898 residues Volume : 268.205 (nm^3) Density : 1013.36 (g/l) Number of solvent molecules: 7689 Processing topology Back Off! I just backed up ./top_input.top to ./#top_input.top.1# GROMACS reminds you: "Catholic School Girls Rule" (Red Hot Chili Peppers) Adding line for 7689 solvent molecules with resname (SOL) to topology file (./top_input.top) :-) 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/075/528/75528529/working Command line: gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn 0 Ignoring obsolete mdp entry 'ns_type' NOTE 1 [file ./ions.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. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file top_input.top, line 31058]: System has non-zero total charge: -6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 56034.00 NOTE 3 [file ./ions.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes GROMACS reminds you: "Misslycka kan man med all kod" (Mats Nylen) Setting the LD random seed to 2105278327 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' Analysing residue names: There are: 208 Protein residues There are: 1 Other residues There are: 7689 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 2 Mb of data :-) GROMACS - gmx genion, 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/075/528/75528529/working Command line: gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc 0.0 -seed 1 Reading file ions.tpr, VERSION 2022-conda_forge (single precision) Reading file ions.tpr, VERSION 2022-conda_forge (single precision) Group 0 ( System) has 26368 elements Group 1 ( Protein) has 3280 elements Group 2 ( Protein-H) has 1636 elements Group 3 ( C-alpha) has 208 elements Group 4 ( Backbone) has 624 elements Group 5 ( MainChain) has 833 elements Group 6 ( MainChain+Cb) has 1026 elements Group 7 ( MainChain+H) has 1039 elements Group 8 ( SideChain) has 2241 elements Group 9 ( SideChain-H) has 803 elements Group 10 ( Prot-Masses) has 3280 elements Group 11 ( non-Protein) has 23088 elements Group 12 ( Other) has 21 elements Group 13 ( G5E) has 21 elements Group 14 ( Water) has 23067 elements Group 15 ( SOL) has 23067 elements Group 16 ( non-Water) has 3301 elements Select a group: Number of (3-atomic) solvent molecules: 7689 Back Off! I just backed up ./top_input.top to ./#top_input.top.2# Using random seed 1. Replacing solvent molecule 154 (atom 3763) with NA Replacing solvent molecule 3152 (atom 12757) with NA Replacing solvent molecule 2760 (atom 11581) with NA Replacing solvent molecule 4227 (atom 15982) with NA Replacing solvent molecule 822 (atom 5767) with NA Replacing solvent molecule 7252 (atom 25057) with NA GROMACS reminds you: "Misslycka kan man med all kod" (Mats Nylen) Will try to add 6 NA ions and 0 CL ions. Select a continuous group of solvent molecules Selected 15: 'SOL' Processing topology Replacing 6 solute molecules in topology file (./top_input.top) by 6 NA and 0 CL ions.