The shortest periodic distance is very small. How to solve this problem without changing box?

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1

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

2

Did you find any solution for this? I’m getting a mindist of 0.5 nm but my non-bonded cutoffs are 0.9 each. I, too, don’t want to change box size. I was thinking maybe arresting the rotation of my protein molecule could help. What do you think?

3

The best solution is changing the unit cell. If the issue is that you have an elongated protein which rotates, you can also remove rotation around the center of mass of the protein.

4

Thank you for your suggestion. I shall try this too. Meanwhile, I increased the distance to box edge from 1.0 nm to 1.5 nm and it helped in correcting the periodic image interaction issue. I’m suffering a decrease in performance, as expected, but it’s not that severe and I could make it work.