# Membrane Equilibrium

**URL:** <https://gromacs.bioexcel.eu/t/membrane-equilibrium/12183>\
**Category:** User discussions\
**Tags:** mdp-parameters, simulation-setup\
**Created:** [June 2, 2025, 5:25am UTC](https://gromacs.bioexcel.eu/t/membrane-equilibrium/12183 "2025-06-02T05:25:21Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![4001goen](https://avatars.discourse-cdn.com/v4/letter/4/bcef8e/32.png) [@4001goen](https://gromacs.bioexcel.eu/u/4001goen)\
**Post date:** [June 2, 2025, 5:25am UTC](https://gromacs.bioexcel.eu/t/membrane-equilibrium/12183/1 "2025-06-02T05:25:21Z")

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GROMACS version: 2021.4  
GROMACS modification: Yes/No  
Here post your question

Hello,

Before proceeding to the production run, I was performing membrane equilibration. Since I expected the deprotonated lipid to migrate toward the membrane core, I planned to monitor box size changes as an indicator of system stabilization. I’ve previously had success using this method for equilibration.

Below is the `.mdp` file I used:

```auto
title = KALP15-DPPC Production MD 
; Run parameters
integrator	= md
nsteps = 50000000
dt = 0.002
; Output control
nstxout = 0
nstvout = 0
nstxtcout	= 30000
nstenergy	= 30000
nstlog = 30000
; Bond parameters
continuation	= yes
constraint_algorithm = lincs
constraints	= h-bonds
lincs_iter	= 1
lincs_order	= 4
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb	= 1.2
rvdw = 1.2
; Electrostatics
coulombtype	= PME
pme_order	= 4
fourierspacing	= 0.16
; Temperature coupling
tcoupl = v-rescale
tc-grps = SOL_ION MEMB
tau_t = 0.5 0.5
ref_t = 300 300
; Pressure coupling
pcoupl = parrinello-rahman
pcoupltype	= semiisotropic
tau_p = 12.0
ref_p = 1.0 1.0
compressibility = 3.0e-5 3.0e-5
; PBC and dispersion correction
pbc = xyz
DispCorr	= EnerPres
; Velocity generation
gen_vel = no
; Center of mass motion removal
nstcomm = 1
comm-mode = Linear
comm-grps = SOL_ION MEMB
refcoord_scaling = com

```

At 300 K, the membrane appeared as follows (attached image).

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/f/fd3e4b7a27dca380d8d5ef6178a58a1a631f98e5.jpeg)

At 300 K, the membrane appeared to be stable and there was no noticeable change in box size or lipid distribution. However, to accelerate equilibration, I increased the temperature to 373 K. Upon doing so, I observed a drastic shrinkage of the box size and elongation of the membrane in the Z-direction, as shown in the image below.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e29480801e0b69dc186d76d5df8a0e31f4e54188.jpeg)  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/4b7622918d99d0f8e8f9df75408528f6267fa5fb.jpeg)

I’m wondering whether this is an expected effect of the elevated temperature or if there might be something incorrectly set in my `.mdp` file. If this issue is due to the temperature increase, would it be more appropriate to simply extend the equilibration time at 300 K instead?

Thank you in advance for your insights!

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**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\
**Post date:** [June 2, 2025, 9:10am UTC](https://gromacs.bioexcel.eu/t/membrane-equilibrium/12183/2 "2025-06-02T09:10:54Z")

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Hi,

which lipid composition for your membrane do you use, and how long are your simulations?

Best,  
Marius

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<div class="post-metadata">

**Author:** ![4001goen](https://avatars.discourse-cdn.com/v4/letter/4/bcef8e/32.png) [@4001goen](https://gromacs.bioexcel.eu/u/4001goen)\
**Post date:** [June 2, 2025, 10:16am UTC](https://gromacs.bioexcel.eu/t/membrane-equilibrium/12183/3 "2025-06-02T10:16:00Z")

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The composition is identical to that of Pfizer’s(BNT162b2) formulation.  
A simulation was conducted at 373 K for approximately 200 ns, during which the membrane underwent the following morphological changes.

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<div class="post-metadata">

**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\
**Post date:** [June 2, 2025, 3:44pm UTC](https://gromacs.bioexcel.eu/t/membrane-equilibrium/12183/4 "2025-06-02T15:44:07Z")

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Was the membrane self-assembled? And what is the lateral size of the membrane at the start of the simulation? I would guess that the migration of the aminolipids into the membrane core lead to a strong shrinkage of the membrane surface area, and at a certain point periodic boundary artefacts come into play. In this [paper](https://doi.org/10.1016/j.bpj.2022.08.037) the authors circumvented this issues by increasing the membrane size.