GROMACS version:2022-cp2k interface
I couldn’t manage my nvt.tpr I tried to fix problem but I couldn’t.
gmx_cp2k grompp -f nvt.mdp -c confout.gro -r confout.gro -p topol.top -n index.ndx -o nvt.tpr
nvt.mdb file :
; md-nvt.mdp - used as input into grompp to generate nma-nvt.tpr
integrator = md ; MD using leap-frog integrator
dt = 0.001 ; 1fs time-step
nsteps = 100 ; 100 fs simulation
; Set output frequency to each step
nstxout = 1 ; Coordinates to trr
nstlog = 1 ; Energies to md.log
nstcalcenergy = 1 ; Energies to ener.edr
nstenergy = 1 ; Energies to ener.edr
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Set cut-offs
rlist = 0.2 ; NB-search cut-off
rcoulomb = 0.2 ; Short-range electrostatic cut-off
rvdw = 0.2 ; Short-range Van der Waals cut-off
;Temperature coupling options
tcoupl = v-rescale
nsttcouple = 1
tc-grps = System
tau-t = 0.1
ref-t = 300
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = yes
gen-temp = 300
gen-seed = -1
; CP2K QMMM parameters
qmmm-cp2k-active = true ; Activate QMMM MdModule
qmmm-cp2k-qmgroup = System ; Index group of QM atoms
qmmm-cp2k-qmmethod = PBE ; Method to use
qmmm-cp2k-qmcharge = 0 ; Charge of QM system
qmmm-cp2k-qmmultiplicity = 1 ; Multiplicity of QM system
ERROR:
Setting the LD random seed to -52773913
Generated 3916 of the 3916 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3916 of the 3916 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘DNA_chain_A’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘mef’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘NA’
turning H bonds into constraints…
Setting gen_seed to -75563652