# RMSD curve of the protein of the lipid bilayer simulation

**URL:** <https://gromacs.bioexcel.eu/t/rmsd-curve-of-the-protein-of-the-lipid-bilayer-simulation/7902>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun, simulation-setup\
**Created:** [December 21, 2023, 8:12pm UTC](https://gromacs.bioexcel.eu/t/rmsd-curve-of-the-protein-of-the-lipid-bilayer-simulation/7902 "2023-12-21T20:12:58Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![Dulaj](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dulaj/32/3408_2.png) [@Dulaj](https://gromacs.bioexcel.eu/u/Dulaj)\
**Post date:** [December 21, 2023, 8:12pm UTC](https://gromacs.bioexcel.eu/t/rmsd-curve-of-the-protein-of-the-lipid-bilayer-simulation/7902/1 "2023-12-21T20:12:58Z")

</div>

GROMACS version: 2023.2  
GROMACS modification: No  
Here post your question

I have done a MD simulation in GROMACS for my protein-lipid bilayer system generated using CHARMM-GUI. Protein is a bacterial fluc channel (5a43), and lipids are DPPC.

During equilibration and also in the production runs, I used V-rescale and C-rescale as the thermostat and barostat respectively. The simulation temperature was 323.15K. Other parameters are usual parameters used in membrane simulations.

I want to confirm whether the RMSD is converged and also I hope for advice from experienced people in present-day MD simulations, about the novel C-rescale barostat. I have seen people are using PR for the production runs often. Is there an advantage of using PR over C-rescale in the production runs? However, I got “pressure scaling is more than 1%” warnings when I was using PR in my previous attempts at this simulation even after the system is equilibrated in m)ultiple steps (as given by CHARMM-GUI mdp files) and longer time scales (1+!+1+5+10+30\* ns - \* without any constraints). I did not get any warinings when I use C-rescale.

Here is the RMSD curve,

 ![1000ns-rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/91cdb273051dc27a2eb5ad4cb3ccbf147d232e43.png)

Here is the final structure achieved by the simulation.

![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/69c086fe82566969733e5395c4bfdc9192028e74.jpeg)

![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a0168647f0c7d7e63458d9133107746660bcb92c.jpeg)

System size,

![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/f/f514998c617df3e1e9f193909a6d2a604f4388f9.png)