# PBC = xy slow performance

**URL:** <https://gromacs.bioexcel.eu/t/pbc-xy-slow-performance/8941>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun, simulation-setup\
**Created:** [April 21, 2024, 10:31am UTC](https://gromacs.bioexcel.eu/t/pbc-xy-slow-performance/8941 "2024-04-21T10:31:05Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![GeorgePkhakadze](https://avatars.discourse-cdn.com/v4/letter/g/6a8cbe/32.png) [@GeorgePkhakadze](https://gromacs.bioexcel.eu/u/GeorgePkhakadze)\
**Post date:** [April 21, 2024, 10:31am UTC](https://gromacs.bioexcel.eu/t/pbc-xy-slow-performance/8941/1 "2024-04-21T10:31:06Z")

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GROMACS version: 2024.1  
GROMACS modification: No  
Here post your question

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

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [April 26, 2024, 2:47pm UTC](https://gromacs.bioexcel.eu/t/pbc-xy-slow-performance/8941/2 "2024-04-26T14:47:29Z")

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I don’t see how it would matter much what PBC conditions you choose, unless you are running at high parallelization. Are you running with domain decomposition and if so, how does the decomposition differ between the two PBC setups?