GROMACS version:2022.1((single precision)
GROMACS modification: Yes/No
Hi Everyone,
Today I am running my second protein ligand simulation(read I am new to GROMACS)
I am using a LINUX server cluster of following configurations:
$ lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 1
Core(s) per socket: 12
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 63
Model name: Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz
Stepping: 2
CPU MHz: 1200.042
BogoMIPS: 4594.33
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 30720K
NUMA node0 CPU(s): 0-11
NUMA node1 CPU(s): 12-23
I am running a protein-ligand simulation of 500ns having the following atoms :
Compound #atoms
Protein 140 residues
ligand 71
SOL 317409 H2O molecules
SOD 9
I used md.mdp file as follows:
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000000 ; 2 * 5000000 = 10000 ps (500 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save coordinates every 10.0 ps
; Bond parameters
continuation = yes ; continuing from NPT
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
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_ligan SOL_SOD ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = no ; continuing from NPT equilibration
I used the command nohup mpiexec -np 24 gmx_mpi mdrun -deffnm md -v, and unbearably, it shows that it will finish Thu Jun 13 04:47:54 2024. Please suggest anything to fasten up the process.
I would be grateful for suggestions/help
Thanks in advance