GROMACS分子模拟基础实验教程(5)-为模拟体系添加离子

; ions.mdp - used as input into grompp to generate ions.tpr; Parameters describing what to do, when to stop and what to saveintegrator  = steep         ; Algorithm (steep = steepest descent minimization)emtol       = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nmemstep      = 0.01          ; Minimization step sizensteps      = 50000         ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactionsnstlist         = 1         ; Frequency to update the neighbor list and long range forcescutoff-scheme   = Verlet    ; Buffered neighbor searchingns_type         = grid      ; Method to determine neighbor list (simple, grid)coulombtype     = cutoff    ; Treatment of long range electrostatic interactionsrcoulomb        = 1.0       ; Short-range electrostatic cut-offrvdw            = 1.0       ; Short-range Van der Waals cut-offpbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions

gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr

Command line:  gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
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.
Setting the LD random seed to -339223553Generated 330891 of the 330891 non-bonded parameter combinationsGenerating 1-4 interactions: fudge = 0.5Generated 330891 of the 330891 1-4 parameter combinationsExcluding 3 bonded neighbours molecule type 'Protein_chain_A'Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 2 [file topol.top, line 18409]:  System has non-zero total charge: 8.000000  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.
Analysing residue names:There are:   129    Protein residuesThere are: 10644      Water residuesAnalysing Protein...Number of degrees of freedom in T-Coupling group rest is 69741.00

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.
This run will generate roughly 3 Mb of data
There were 3 notes

gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

Select a group: 13Selected 13: 'SOL'Number of (3-atomic) solvent molecules: 10644         
Processing topologyReplacing 8 solute molecules in topology file (topol.top)  by 0 NA and 8 CL ions.

Back Off! I just backed up topol.top to ./#topol.top.2#Using random seed -17825805.Replacing solvent molecule 5584 (atom 18712) with CLReplacing solvent molecule 1421 (atom 6223) with CLReplacing solvent molecule 6259 (atom 20737) with CLReplacing solvent molecule 4884 (atom 16612) with CLReplacing solvent molecule 1956 (atom 7828) with CLReplacing solvent molecule 5631 (atom 18853) with CLReplacing solvent molecule 137 (atom 2371) with CLReplacing solvent molecule 3672 (atom 12976) with CL          

Replacing 8 solute molecules in topology file (topol.top)  by 0 NA and 8 CL ions.