GROMACS version:2020.6
GROMACS modification: No
1.Why changes in rlist happen when I run the same thing in a GPU vs CPU?
2.I have set the r-list and nst-list value in the parameters files , yet why they change. And do these changes has any impact on the results?
- GPU
gmx mdrun -deffnm complex_nvt -v -nt 64
Reading file complex_nvt.tpr, VERSION 2020.2-dev-20200430-5e78835-unknown (single precision)
Changing nstlist from 5 to 100, rlist from 1.2 to 1.346
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 64 OpenMP threads
- CPU
gmx mdrun -deffnm complex_nvt -v
Reading file complex_nvt.tpr, VERSION 2020.6 (single precision)
Changing nstlist from 5 to 80, rlist from 1.2 to 1.322
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 12 OpenMP threads
These are my parameters- nvt-
vi nvt
title = NVT
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
cutoff-scheme = Verlet
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = ATG4B LC3B SOL_NA ; two coupling groups - more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = ATG4B LC3B SOL_NA
I am new to gromacs and would really appreciate the help.
Thank You in advance!