; minim.mdp - used as input into grompp to generate em.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     = PME       ; 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 minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr

Command line:  gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr

Ignoring obsolete mdp entry 'ns_type'

NOTE 1 [file minim.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 -58878020Generated 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'Excluding 1 bonded neighbours molecule type 'CL'Analysing residue names:There are:   129    Protein residuesThere are: 10636      Water residuesThere are:     8        Ion residuesAnalysing Protein...Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...Number of degrees of freedom in T-Coupling group rest is 69717.00Calculating fourier grid dimensions for X Y ZUsing a fourier grid of 60x60x60, spacing 0.117 0.117 0.117Estimate for the relative computational load of the PME mesh part: 0.26This run will generate roughly 3 Mb of data

gmx mdrun -v -deffnm em

Steepest Descents:   Tolerance (Fmax)   =  1.00000e+03   Number of steps    =        50000Step=    0, Dmax= 1.0e-02 nm, Epot= -3.31916e+05 Fmax= 2.28198e+05, atom= 1905Step=    1, Dmax= 1.0e-02 nm, Epot= -3.47978e+05 Fmax= 8.64638e+04, atom= 19877Step=    2, Dmax= 1.2e-02 nm, Epot= -3.70296e+05 Fmax= 3.30123e+04, atom= 19877Step=    3, Dmax= 1.4e-02 nm, Epot= -3.98673e+05 Fmax= 1.32088e+04, atom= 24182Step=    4, Dmax= 1.7e-02 nm, Epot= -4.27120e+05 Fmax= 5.66426e+03, atom= 21851…………………………………………Step=  858, Dmax= 6.3e-03 nm, Epot= -5.87436e+05 Fmax= 5.31422e+03, atom= 736Step=  859, Dmax= 7.6e-03 nm, Epot= -5.87449e+05 Fmax= 6.33299e+03, atom= 736Step=  860, Dmax= 9.1e-03 nm, Epot= -5.87458e+05 Fmax= 7.67593e+03, atom= 736Step=  861, Dmax= 1.1e-02 nm, Epot= -5.87465e+05 Fmax= 9.09571e+03, atom= 736Step=  863, Dmax= 6.5e-03 nm, Epot= -5.87517e+05 Fmax= 9.81522e+02, atom= 736

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 864 stepsPotential Energy  = -5.8751662e+05Maximum force     =  9.8152197e+02 on atom 736Norm of force     =  2.0807849e+01

; minim.mdp - used as input into grompp to generate em.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

Command line:  gmx energy -f em.edr -o potential.xvg
Opened em.edr as single precision energy file
Select the terms you want from the following list byselecting either (part of) the name or the number or a combination.End your selection with an empty line or a zero.-------------------------------------------------------------------  1  Bond             2  Angle            3  Proper-Dih.      4  Ryckaert-Bell.  5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8  Coulomb-(SR)   9  Coul.-recip.    10  Potential       11  Pressure        12  Vir-XX        13  Vir-XY          14  Vir-XZ          15  Vir-YX          16  Vir-YY        17  Vir-YZ          18  Vir-ZX          19  Vir-ZY          20  Vir-ZZ        21  Pres-XX         22  Pres-XY         23  Pres-XZ         24  Pres-YX       25  Pres-YY         26  Pres-YZ         27  Pres-ZX         28  Pres-ZY       29  Pres-ZZ         30  #Surf*SurfTen   31  T-rest

Last energy frame read 725 time  916.000         
Statistics over 917 steps [ 0.0000 through 916.0000 ps ], 1 data setsAll statistics are over 726 points (frames)
Energy                      Average   Err.Est.       RMSD  Tot-Drift-------------------------------------------------------------------------------Potential                   -566593      11000    28032.5   -73338.4  (kJ/mol)

@    title "GROMACS Energies"@    xaxis  label "Time (ps)"@    yaxis  label "(kJ/mol)"@TYPE xy@ view 0.15, 0.15, 0.75, 0.85@ legend on@ legend box on@ legend loctype view@ legend 0.78, 0.8@ legend length 2@ s0 legend "Potential"    0.000000  -331915.562500    1.000000  -347978.500000    2.000000  -370295.875000    3.000000  -398672.937500    4.000000  -427119.781250    5.000000  -452107.750000    ………………………………    ………………………………          

apt-get install grace

xmgrace potential.xvg