GROMACS version: 2024
GROMACS modification: No
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The shortest periodic distance is 0.14175 (nm). The box used is rectangle box with PBC
gmx mindist -f md_0_30.xtc -s md_0_30.tpr -pi
:-) GROMACS - gmx mindist, 2024 (-:
Executable: /opt/gromacs2024gpu/bin/gmx
Data prefix: /opt/gromacs2024gpu
Working dir: /home/dell/Videos/4BA.4.5_PW570_cmplx/charmm27/PW570_D
Command line:
gmx mindist -f md_0_30.xtc -s md_0_30.tpr -pi
Choose a group for distance calculation
Reading file md_0_30.tpr, VERSION 2024 (single precision)
Reading file md_0_30.tpr, VERSION 2024 (single precision)
Group 0 ( System) has 92051 elements
Group 1 ( Protein) has 9496 elements
Group 2 ( Protein-H) has 4835 elements
Group 3 ( C-alpha) has 623 elements
Group 4 ( Backbone) has 1869 elements
Group 5 ( MainChain) has 2489 elements
Group 6 ( MainChain+Cb) has 3065 elements
Group 7 ( MainChain+H) has 3083 elements
Group 8 ( SideChain) has 6413 elements
Group 9 ( SideChain-H) has 2346 elements
Group 10 ( Prot-Masses) has 9496 elements
Group 11 ( non-Protein) has 82555 elements
Group 12 ( Water) has 82545 elements
Group 13 ( SOL) has 82545 elements
Group 14 ( non-Water) has 9506 elements
Group 15 ( Ion) has 10 elements
Group 16 ( Water_and_ions) has 82555 elements
Select a group: 1
Selected 1: ‘Protein’
Last frame 300 time 30000.000
The shortest periodic distance is 0.14175 (nm) at time 800 (ps),
between atoms 3655 and 8757
; Run parameters in md.mdp
integrator = md ; leap-frog integrator
nsteps = 15000000 ; 2 * 15000000 = 30000 ps (30 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 50000 ; save energies every 100.0 ps
nstlog = 50000 ; update log file every 100.0 ps
nstxout-compressed = 50000 ; save compressed coordinates every 100.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
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
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; 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