GROMACS version: 2024.2
GROMACS modification: No
Hello! I have been trying to run an NVT step for my atomistic and coarse grained simulations, and the process has been running incredibly slow (<0.01 ns/day). They are running and producing reasonable trajectories. I was wondering if anyone who is more familiar with NVT could aid in seeing what I am doing run.
For simulation specifications, I am running both a coarse grained and an atomistic run. I am running on an A100 GPU (Top of the line). Atomistic simulation is ~980000 molecules, coarse grained is ~70000. Both are running around the same speed. Energy minimization step ran fine and fast for both. No warnings popped up. Commands:
#SBATCH elements:
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1
#SBATCH --partition=gpu # gpu node(s)
Atomistic: # Run NVT
gmx_mpi grompp -f NVT.mdp -c EM.gro -p 8HKQAtom00N00K00Z.top -o NVT.tpr -maxwarn 4
srun gmx_mpi mdrun -v -deffnm NVT
Atomistic NVT file:
integrator = md
dt = 0.002
nsteps = 100000000
nstxout-compressed = 10000
compressed-x-precision = 1000
nstlog = 5000
nstenergy = 5000
nstcalcenergy = 500
cutoff-scheme = verlet
nstlist = 5
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.2
epsilon_r = 15
epsilon_rf = 0
vdw_type = Cut-off
vdw-modifier = Potential-shift-verlet
rvdw = 1.2
tcoupl = v-rescale
tc-grps = Protein Non-Protein
tau-t = 1.0 1.0
ref-t = 310 310
gen-temp = 310
Pcoupl = no
gen-vel = yes
continuation = no
constraints = all-bonds
constraint_algorithm = Lincs
lincs_order = 4
lincs_warnangle = 90
Coarse grained: # Run NVT
gmx_mpi grompp -f NVT.mdp -c EM.gro -p 8HKQCoarse00N00K00Z.top -o NVT.tpr -maxwarn 4
srun gmx_mpi mdrun -v -deffnm NVT
Coarse grained NVT file:
integrator = md
dt = 0.002
nsteps = 100000000
nstxout-compressed = 10000
compressed-x-precision = 5000
nstlog = 5000
nstenergy = 5000
nstcalcenergy = 500
cutoff-scheme = verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.2
epsilon_r = 15
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.2
tcoupl = v-rescale
tc-grps = Protein Non-Protein
tau-t = 1.0 1.0
ref-t = 310 310
gen-temp = 310
Pcoupl = no
gen-vel = yes
continuation = no
constraints = none
constraint_algorithm = Lincs
lincs_order = 4
lincs_warnangle = 90