# \[Errors\] Problems during Umbrella Sampling

**URL:** <https://gromacs.bioexcel.eu/t/errors-problems-during-umbrella-sampling/13169>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun, umbrella-sampling\
**Created:** [February 1, 2026, 7:59pm UTC](https://gromacs.bioexcel.eu/t/errors-problems-during-umbrella-sampling/13169 "2026-02-01T19:59:36Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![grahzdan](https://avatars.discourse-cdn.com/v4/letter/g/9d8465/32.png) [@grahzdan](https://gromacs.bioexcel.eu/u/grahzdan)\
**Post date:** [February 1, 2026, 7:59pm UTC](https://gromacs.bioexcel.eu/t/errors-problems-during-umbrella-sampling/13169/1 "2026-02-01T19:59:36Z")

</div>

GROMACS version: 2022.3-plumed\_2.8.1  
GROMACS modification: Yes/ **No**

Hi all,

I am having an assignment to do simple Umbrella Sampling simulation to calculate Free energy profile for martinized (Martini 3) small peptide and simple POPC membrane bilayer. I tried pushing the peptide all teh way through the membrane, but the pmf is very unsymmetrical and I seem to have holes in my windows which I dont know how to fill. Also I find it weird that the peptide doesnt want to adsorb to the membrane at all.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/41664411834ed088d273138640314929bdd3c56d.png)

I tried adding more windows and widening them but I still have a hole there.

I was then recomended to run steered simulation on just one side and pull away from one of the sides of the membrane, but trying that I am not able run the sim at all. I mostly encountered this error and have no clue how to fix it  
“Fatal error: Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = 1 1 8, box vector[3] = -nan -nan -nan”

pull.mdp used:

```auto
integrator = md
tinit = 0.0
dt = 0.020
nsteps = 2000000

nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000
nstxout-compressed = 5000
compressed-x-precision = 100

cutoff-scheme = Verlet
nstlist = 20

ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

tcoupl = v-rescale
tc-grps = system
tau_t = 1.0
ref_t = 310.15

; Pressure coupling:
Pcoupl = Parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
refcoord_scaling = com

; COM pulling
pull = yes
pull-nstxout = 1000
pull-nstfout = 1000
pull-ngroups = 2
pull-group1-name	= POPC
pull-group2-name	= Protein
pull-ncoords = 1
pull-coord1-type	= umbrella
pull-coord1-geometry	= cylinder
pull-cylinder-r = 1.5

pull-coord1-groups	= 1 2
pull-coord1-dim = N N Y
pull-coord1-vec = 0 0 -1

pull-coord1-start = yes ; Start from initial distance
pull-coord1-init = 0
pull-coord1-rate = 0.0001 ; Pulling rate in nm/ps
pull-coord1-k = 1000 ; Spring constant in kJ/mol/nm^2

```

us.mdp used:

```auto
define = 
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 25000000
comm-mode =	Linear
nstcomm =	100
comm-grps =	system

nstlog = 10000
nstenergy = 1000
nstxout-compressed = 10000
compressed-x-precision = 1000

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

tcoupl = v-rescale
tc-grps = system

tau_t = 1.0
ref_t = 310.15 

; Pressure coupling:
Pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no

refcoord_scaling = all

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; COM Pulling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
pull =	yes
pull-nstxout	=	100
pull-nstfout	=	100

pull-ngroups	=	2
pull-group1-name	= POPC
pull-group2-name	=	Protein

pull-ncoords	=	1
pull-cylinder-r	=	1.2

pull-coord1-k	=	<FC>
pull-coord1-type	=	umbrella
pull-coord1-geometry	=	cylinder
pull-coord1-groups	= 1 2
pull-coord1-dim	=	N N Y
pull-coord1-vec	=	0.0	0.0	1.0
pull-coord1-start	=	no
pull-coord1-rate	=	0.00
pull_coord1_init = <CV>

```

Thank you so much in advance

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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:** [February 4, 2026, 9:08am UTC](https://gromacs.bioexcel.eu/t/errors-problems-during-umbrella-sampling/13169/2 "2026-02-04T09:08:49Z")

</div>

When you have gaps you need a higher force constant and thus narrower, more tightly spaced umbrellas (not wider umbrellas).

At which step does the error occur?