GROMACS version:2025.0
GROMACS modification: No
Hello everyone
Need your help for setting nvt.mdp for imprinted polymer MD simulation
So i wanna start MD simulation like synthesis in laboratory which is start at 298.15K (25C) to 343.15K (70C)
I try to using annealing but always failed, do you mind give me suggestion for my nvt.mdp file?
Thank you very much for your help
define =
constraints = all-bonds
constraint_algorithm = lincs
lincs_iter = 2
lincs_order = 4
integrator = md
dt = 0.001 ; ps
nsteps = 1000000 ; total nsteps x dt = 1.0 ns
nstcomm = 1 ; stop translation of box center of mass
comm_mode = Linear
comm_grps = system
; Data saving frequencies (reduce output file size)
nstxout = 10000 ; Save trajectory every 10 ps
nstvout = 10000 ; Save velocity data every 10 ps
nstlog = 10000 ; Save log data every 10 ps
nstenergy = 10000 ; Save energy data every 10 ps
nstcalcenergy = 100 ; Calculate energy every 100 steps to reduce data output
nstxout-compressed = 20000 ; Save compressed trajectory every 20 ps
compressed-x-grps = system ; Compress trajectory to save space
cutoff-scheme = verlet
nstlist = 50 ; Increased for better accuracy in larger systems
ns_type = grid
rlist = 1.4 ; Slightly increased cutoff for better accuracy
coulombtype = pme
rcoulomb = 1.4 ; Increased Coulomb cutoff
rvdw = 1.4 ; Increased Van der Waals cutoff
DispCorr = EnerPres
pme_order = 4
fourierspacing = 0.15
; Temperature control (maintain at 25°C initially)
tcoupl = v-rescale
tc-grps = system
tau_t = 1.0 ; Smoother temperature control for stability
ref_t = 298.15 ; 25°C target temperature
; Temperature annealing settings (from 25°C to 70°C)
annealing = single
annealing_npoints = 2
annealing_time = 500000 500000 ; Ramp-up time (in steps) for gradual increase
annealing_t = 298.15 343.15 ; Ramp from 25°C (298.15 K) to 70°C (343.15 K)
Pcoupl = no
pbc = xyz
; No velocity generation (continuation from previous run)
gen_vel = no
gen_temp = 298.15 ; Starting temperature taken from previous equilibration
gen_seed = 173529