GROMACS version: 2021.2
GROMACS modification: Yes/No
Hi, I am trying to simulate a protein complex in a water box - the outputs I have obtained directly from CHARMM-GUI using the martini 3.0 forcefield.
When I try to minimise the system, grompp stops prematurely (seemingly during the generation of interactions) and does not output a tpr file. It also does not give any error messages in the console so I am not sure where I can even start troubleshooting. It did output a mdout.tpr though.
Here is what was in the console:
Command line:
gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_charmm2gmx.pdb -r step3_charmm2gmx.pdb -p system.top -n index.ndx -v
Ignoring obsolete mdp entry ‘ns_type’
checking input for internal consistency…
NOTE 1 [file step4.0_minimization.mdp]:
Setting tcoupl from ‘V-rescale’ to ‘no’. Temperature coupling does not
apply to steep.
NOTE 2 [file step4.0_minimization.mdp]:
Setting pcoupl from ‘Berendsen’ to ‘no’. Pressure coupling does not apply
to steep.
Setting the LD random seed to -537139330
processing topology…
Generated 1689 of the 357435 non-bonded parameter combinations
These are the mdp options
define = -DPOSRES -DPOSRES_FC=0 -DNORMANG
integrator = steep
tinit = 0.0
dt = 0.020
nsteps = 3000
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 = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = protein solute
tau_t = 1.0 1.0
ref_t = 303.15 303.15
; Pressure coupling:
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = yes
gen_temp = 303.15
gen_seed = 7388478180
refcoord_scaling = all
;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
What should I do to start troubleshooting? I tried running another different system with different proteins I have with elnedyn22 ff and grompp works fine so I am assuming it is something to do with martini3?