GROMACS version: 2022.04
GROMACS modification: No
Here post your question
Hello.
Im using CHARMM-GUI server to create a combination between my transmembrane peptide an a bilayer composed by 3 different phospholipids (POPS, POPC, POPE). Once i already want to perform my MD according to protocol obtained from the README file, minimization soft-core crash and cant go ahead. The error that appears correspond to :
Fatal error: There are perturbed non-bonded pair interactions beyond the pair-list cutoff of 2.1 nm, which is not supported. This can happen because the system is unstable or because intra-molecular interactions at long distances are excluded. If the latter is the case, you can try to increase nstlist or rlist to avoid this.The error is likely triggered by the use of couple-intramol=no and the maximal distance in the decoupled molecule exceeding rlist.
The same README file suggest changing rvdw and rcoulomb if that error appears. But still failing by the same error
If you encountered “There are 1 perturbed non-bonded pair interaction …” error message,
please modify rvdw and rcoulomb values from 1.1 to 2.0 in the step6.0_minimization.mdp file.
Im adding Soft-core Minimization file content, in case you notice something out of place or wrong :
Soft-Core Minimization file
define = -DFLEXIBLE
integrator = steep
tinit = 0.0
nsteps = 500000
nstlog = 100
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 2.2
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 2.2
tcoupl = v-rescale
tc-grps = protein membrane solute
tau_t = 1.0 1.0 1.0
ref_t = 309.65 309.65 309.65
; Pressure coupling:
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = yes
gen_temp = 309.65
gen_seed = 6924814221
;soft-core-minimization so that single precision GROMACS works here
; Free energy parameters
free-energy = yes
init-lambda = 0.01
sc-alpha = 4
sc-power = 2
sc-coul = yes
nstdhdl = 0
couple-moltype = system
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw-q
; in the final state, both are off.
couple-lambda1 = none
couple-intramol = yes
refcoord_scaling = all
README FILE
#!/bin/csh
Generated by CHARMM-GUI (http://www.charmm-gui.org)
1) Use Gromacs 5.1 or newer to run these simulations
Minimization
setenv GMX_MAXCONSTRWARN -1
step6.0 - soft-core minimization
If you encountered “There are 1 perturbed non-bonded pair interaction …” error message,
please modify rvdw and rcoulomb values from 1.1 to 2.0 in the step6.0_minimization.mdp file
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_charmm2gmx.pdb -r step5_charmm2gmx.pdb -p system.top -n index.ndx -maxwarn 1
gmx mdrun -deffnm step6.0_minimization
step6.1
gmx grompp -f step6.1_minimization.mdp -o step6.1_minimization.tpr -c step6.0_minimization.gro -r step5_charmm2gmx.pdb -p system.top -n index.ndx -maxwarn 1
gmx mdrun -deffnm step6.1_minimization
unsetenv GMX_MAXCONSTRWARN
Equilibration
set cnt = 2
set cntmax = 6
while ( {cnt} <= {cntmax} )
@ pcnt = ${cnt} - 1
if (cnt == 2) then
gmx grompp -f step6.{cnt}_equilibration.mdp -o step6.{cnt}_equilibration.tpr -c step6.{pcnt}_minimization.gro -r step5_charmm2gmx.pdb -p system.top -n index.ndx
else
gmx grompp -f step6.{cnt}_equilibration.mdp -o step6.{cnt}_equilibration.tpr -c step6.{pcnt}_equilibration.gro -r step5_charmm2gmx.pdb -p system.top -n index.ndx
endif
gmx mdrun -deffnm step6.{cnt}_equilibration
@ cnt += 1
end
Production
gmx grompp -f step7_production.mdp -o step7_production.tpr -c step6.6_equilibration.gro -p system.top -n index.ndx
gmx mdrun -deffnm step7_production
Thanks you,