# With Verlet lists only full pbc or pbc=xy with walls is supported

**URL:** <https://gromacs.bioexcel.eu/t/with-verlet-lists-only-full-pbc-or-pbc-xy-with-walls-is-supported/12716>\
**Category:** User discussions\
**Created:** [September 30, 2025, 1:50pm UTC](https://gromacs.bioexcel.eu/t/with-verlet-lists-only-full-pbc-or-pbc-xy-with-walls-is-supported/12716 "2025-09-30T13:50:05Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![VERA](https://avatars.discourse-cdn.com/v4/letter/v/b3f665/32.png) [@VERA](https://gromacs.bioexcel.eu/u/VERA)\
**Post date:** [September 30, 2025, 1:50pm UTC](https://gromacs.bioexcel.eu/t/with-verlet-lists-only-full-pbc-or-pbc-xy-with-walls-is-supported/12716/1 "2025-09-30T13:50:05Z")

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GROMACS version: 2023.3  
GROMACS modification: Yes/No  
Here post your question

Hi All,

I have created an implicit wall for this protein modeled from smog server in Z direction by implementing wall option in the .mdp file.However, with walls I have given the option for the pbc =xy. Need to run a coarse gain simulation with this system by using the following .mdp file .

; Run parameters  
integrator = sd  
nsteps = 100000000  
dt = 0.0005  
; Output control  
nstxout = 10000 ; save coordinates every 1.0 ps  
nstvout = 10000 ; save velocities every 1.0 ps  
nstenergy = 10000 ; save energies every 1.0 ps  
nstlog = 10000 ; update log file every 1.0 ps  
xtc-grps = system ; save the whole system  
energygrps = system ;group(s) to write to energy file  
; Neighborsearching  
ns\_type=grid  
nstlist = 20 ; 20 fs, largely irrelevant with Verlet scheme  
rlist = 1.6 ;treatment of electrostatic interactions  
rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm)  
rvdw = 1.5 ; short-range van der Waals cutoff (in nm)  
; Electrostatics  
cutoff-scheme = verlet  
coulombtype = Cut-off ;Make a grid in the box and only check atoms in neighboring grid cells  
; Temperature coupling is on  
tc-grps = system ; two coupling groups - more accurate  
tau\_t = 1.0 ; Temperature coupling time constant. Smaller values = stronger coupling  
ref\_t = 90.0 ; reference temperature, one for each group, in K  
; Pressure coupling is off  
pcoupl = no  
; Periodic boundary conditions  
pbc = xy  
verlet-buffer-tolerance = -1  
;walls  
nwall = 1  
wall-type = 9-3  
wall-atomtype = X  
wall-density = 100  
wall-r-linpot = 1.00  
; Set wall position explicitly (bottom only)  
wall-ewald-zfac = 3  
; Velocity generation  
gen\_vel = yes ; Velocity generation is on  
gen\_temp = 90.0  
gen\_seed = -1  
ld\_seed = -1  
comm\_mode = none ; center of mass velocity removal.

After running this script the following was the result.

With Verlet lists only full pbc or pbc=xy with walls is supported.

Can somebody tell how to get rid of this error?.

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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:** [October 16, 2025, 9:55am UTC](https://gromacs.bioexcel.eu/t/with-verlet-lists-only-full-pbc-or-pbc-xy-with-walls-is-supported/12716/2 "2025-10-16T09:55:35Z")

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You need to have walls on both sides: nwall=2