GROMACS version: 2024.4
GROMACS modification: Yes/No
Hello,experts! When I conduct “gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr” using nvt.mdp version1. Here is one fatal error:Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values and when I change my nvt.mdp file to version 2, the fatal error becomes: Parameter “tcoupl” doubly defined. The two version of nvt.mdp files are listed below. I guess maybe there are some problems in my molecule str. file generated by CGenFF?
The first version of nvt.mdp reads as following:
; GROMACS .mdp file for NVT equilibration
; Parameters for the run
integrator = md ; Leap-frog integrator
nsteps = 50000 ; Number of steps
dt = 0.002 ; Time step of 2 fs
; Energy minimization and constraints
emtol = 1000.0 ; Stop minimization when energy change < 1000 kJ/mol
emstep = 0.01 ; Initial minimization step size
niter = 50000 ; Maximum number of iterations
; Temperature coupling
tcoupl = nose-hoover ; Temperature coupling method
tau_t = 0.1 ; Relaxation time constant for temperature coupling
ref_t = 300 ; Desired temperature in K
; Pressure coupling (if applicable)
; If you only want NVT (constant volume), this section can be removed
; If you need NPT (constant pressure and temperature), use the following
; tcoupl = nose-hoover ; Pressure coupling method
; tau_p = 1.0 ; Relaxation time constant for pressure coupling
; ref_p = 1.0 ; Desired pressure in bar
; compressibility = 4.5e-5 ; Isothermal compressibility
; Neighbor searching
nstlist = 10 ; Frequency to update the neighbor list
rlist = 1.0 ; Cut-off for neighbor list
coulombtype = pme ; PME for long-range electrostatics
rcoulomb = 1.2 ; Short-range electrostatic cut-off
vdwtype = cut-off ; Van der Waals interaction cut-off
rvdw = 1.2 ; Short-range cut-off for van der Waals
; Output control
nstxout = 5000 ; Save coordinates every 5000 steps
nstvout = 5000 ; Save velocities every 5000 steps
nstfout = 0 ; No force output
nstlog = 1000 ; Save energy and progress every 1000 steps
nstenergy = 1000 ; Save energy every 1000 steps
energygrps = BUTYA SOL ; Energy group for analysis
; Constraints
constraints = h-bonds ; Use only hydrogen bonds constraints
The second version of nvt.mdp reads like this:
; GROMACS .mdp file for NVT equilibration
; Parameters for the run
integrator = md ; Leap-frog integrator
nsteps = 50000 ; Number of steps
dt = 0.002 ; Time step of 2 fs
; Energy minimization and constraints
emtol = 1000.0 ; Stop minimization when energy change < 1000 kJ/mol
emstep = 0.01 ; Initial minimization step size
niter = 50000 ; Maximum number of iterations
; Temperature coupling
tcoupl = nose-hoover ; Use Nose-Hoover chain
tau_t = 0.1 ; Relaxation time constant for temperature coupling
ref_t = 300 ; Desired temperature in K
; Pressure coupling
tcoupl = nose-hoover ; Recommended for pressure coupling
tau_p = 1.0 ; Relaxation time constant for pressure coupling
ref_p = 1.0 ; Desired pressure in bar
compressibility = 4.5e-5 ; Isothermal compressibility of water in bar^-1
; Neighbor searching
nstlist = 10 ; Frequency to update the neighbor list
rlist = 1.0 ; Cut-off for neighbor list
coulombtype = pme ; PME for long-range electrostatics
rcoulomb = 1.2 ; Short-range electrostatic cut-off
vdwtype = cut-off ; Van der Waals interaction cut-off
rvdw = 1.2 ; Short-range cut-off for van der Waals
; Output control
nstxout = 5000 ; Save coordinates every 5000 steps
nstvout = 5000 ; Save velocities every 5000 steps
nstfout = 0 ; No force output
nstlog = 1000 ; Save energy and progress every 1000 steps
nstenergy = 1000 ; Save energy every 1000 steps
energygrps = BUTYA SOL ; Energy group for analysis
; Constraints
constraints = h-bonds ; Use only hydrogen bonds constraints
The error has nothing to do with the molecule topology. You have defined tcoupl
twice. The second instance appears to simply be a typo in which you are using tcoupl
instead of pcoupl
(and you will also need to set an appropriate method, because Nosé-Hoover is a thermostat not a barostat).
Thanks for replying, I change my nvt.mdp file like this and it seems work:
; GROMACS .mdp file for NVT equilibration
; Parameters for the run
integrator = md ; Leap-frog integrator
nsteps = 50000 ; Number of steps (100 ps)
dt = 0.002 ; Time step (2 fs)
; Output control
nstxout = 5000 ; Save coordinates every 5000 steps
nstvout = 5000 ; Save velocities every 5000 steps
nstenergy = 5000 ; Save energy every 5000 steps
nstlog = 5000 ; Save log every 5000 steps
; Bond parameters
continuation = no ; First dynamics run
constraint_algorithm= lincs ; Holonomic constraints
constraints = all-bonds ; All bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; Accuracy of LINCS
lincs_order = 4 ; LINCS accuracy
; Neighbor search
cutoff-scheme = Verlet
ns_type = grid ; Neighbor search method
nstlist = 10 ; Frequency for updating the neighbor list
rcoulomb = 1.2 ; Short-range electrostatic cutoff
rvdw = 1.2 ; Short-range van der Waals cutoff
; Electrostatics
coulombtype = PME ; Use Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; PME interpolation order
fourierspacing = 0.16 ; Grid spacing for PME
; Temperature coupling
tcoupl = nose-hoover ; Nose-Hoover thermostat
tau_t = 0.1 ; Relaxation time constant for temperature coupling
ref_t = 298 ; Desired temperature in K
tc-grps = System ; Group(s) to couple temperature to (e.g., ‘System’)
; Pressure coupling
pcoupl = no ; No pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3D periodic boundary conditions
; Dispersion correction
DispCorr = EnerPres ; Apply dispersion correction for cut-off scheme
; Velocity generation
gen_vel = yes ; Assign velocities from Maxwell distribution
gen_temp = 298 ; Temperature for Maxwell distribution
gen_seed = -1 ; Random seed for velocity generation
I find it just like what you point out! Thank you! I now understand!!!