GROMACS version: 2023.1
GROMACS modification: Yes/No
Hi. When I did NVT heating in gromacs 2022.4 and 2023.1 versions with the same .mdp file,
In 2023.1 version, I received these error message.
Program: gmx mdrun, version 2023.1
Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674)
Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting)::<lambda()>
Assertion failed:
Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable
At this point in the code the ensemble temperature setting cannot be auto
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
On the other hand, in the 2022.4 version, the NVT process proceeds without any error messages despite using the same .mdp file.
And when I removed the Annealing for gradual heating (annealing, annealing_npoints, annealing_time, annealing_temp) part of the .mdp file in version 2023.1, I saw that it ran without any error messages.
Why is this happening? Is there something I’m missing?
This is .mdp options which I use.
; Protein-ligand complex NVT heating
;define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
dt = 0.002 ; 2 fs
nsteps = 30000 ; 2 * 30000 = 60 ps
; Output control
nstlog = 1000 ; update log file every 2.0 ps
nstenergy = 1000 ; save energies every 2.0 ps
nstxout-compressed = 1000 ; save .xtc file
; Neighborsearching
cutoff-scheme = Verlet ; Don’t set rlist, verlet-buffer-tolerance
nstlist = 20 ; will be automatically increased by mdrun, usually to 20 or more
ns_type = grid ; search neighboring grid cells
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
; Van der Waals
vdw-type = Cut-off
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_QM1Z Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant for coupling in ps
ref_t = 300 300 ; reference temperature for coupling, one for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; Annealing for gradual heating
annealing = single single ; a single sequence of annealing
annealing_npoints = 6 6 ; the number of reference/constrol points
annealing_time = 0 10 20 30 40 50 0 10 20 30 40 50
annealing_temp = 10 70 130 190 250 300 10 70 130 190 250 300
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 10 ; temperature for Maxwell distribution
gen_seed = 54321 ; generate a random seed
ld-seed = 54321 ; seed for random number generation for langevan dynamics