Hi Everyone,
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
You can ask your questions in the GROMACS forum and get your answer directly from gmx experts: https://gromacs.bioexcel.eu/
Farzane Jalalypour , I have asked the question there also but nobody is replying . Any idea you have and would like to share to speed up from present 2ns/day ?
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