GROMACS version: 2024.1
GROMACS modification: No
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Good time of the day. I am currently running membrane simulations using CGMartini. When using PBC = xy the performance is around 3 times slower than PBC = xyz.
Is there a way to increase performance in this case? It feels that PBC = xyz and xy are not too dissimilar, so I am thinking it could be a problem with my mdp parameters.
Here are the parameters for the mdp file:
title = Martini
integrator = md
dt = 0.01
nsteps = 34000000
nstcomm = 100
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 250000 ; Output frequency for energies to log file
nstenergy = 250000 ; Output frequency for energies to energy file
nstxtcout = 250000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps = POPC POPG W ION protein
energygrps =
cutoff-scheme = Verlet
nstlist = 150
ns_type = grid
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff ;(for use with Verlet-pairlist)
vdw-modifier = Potential-shift-verlet
rvdw = 1.1 ;(for use with Verlet-pairlist)
tcoupl = v-rescale
tc-grps = POPC POPG W ION protein
tau_t = 1.0 1.0 1.0 1.0 1.0
ref_t = 310 310 310 310 310
Pcoupl = no ; parrinello-rahman
gen_vel = yes
gen_temp = 310
gen_seed = -1
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
pbc = xy
nwall = 2
wall-atomtype = W W
wall-density = 6 6
wall-r-linpot = -1