Re-centering the protein in the box after MD simulation

User discussions
1

I have a dimer protein with its crystal structure available. I have performed MD simulation for the same for 100 ns. While performing RMSD analysis, the plot that I have got looks unusual inferring to protein moving out of the box.
I tried to re center the protein by using the following command: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center, but it didn’t change the rmsd plot.

How should I proceed to re center this protein?

RMSD
RMSD792×612 5.42 KB

2

Hi,
Here you can find a workflow to fix periodicity effects and center your system Terminology — GROMACS 2022 documentation

You can also search the tag gmx-trjconv. You can find posts in the forum that address similar problems (maybe you saw them already or maybe not)
https://gromacs.bioexcel.eu/tag/gmx-trjconv

I hope it helps
Alessandra

3

Two steps :

  1. gmx trjconv -pbc whole -f *.xtc -o *_whole.xtc -s *.tpr
  2. gmx trjconv -pbc mol -center -f *_whole.xtc -o *_whole_nopbc.xtc -s *.tpr

This works for a monomer protein, might work for your system

4

Hii,
Thank you for your response.
Yes I did check the posts on the forum discussing the same problem and tried using same commands. But somehow, the RMSD plot didnot get any better.
The reference file I am using with -s is md_0_1.tpr, can I use any other .tpr or .gro file for centering my protein?

5

Thank you Marvin.

I did try it, but looks like it doesn’t change my RMSD plot. Which .tpr file have you used? can I se nvt/npt.tpr file as a reference for plotting the RMSD?

6

tpr file is a binary file. you can dump the pdb file from the tpr. To find the RMSD, you need the crystal structure as a pdb file. If crystal structure is not present then an average structure(from your trajectory) can be used as a reference structure.

7

Heya,

Take a look at the post I made a while ago at the 3rd party tools section of this forum. mdvwhole will solve your problem and you do not need to fiddle with your trajectory. I do not know how you solvent is named, but after installing (takes a while as I did not clean the dependencies yet…) you should run the following command replacing WATER and IONS with their respective residue names in your system:

mdvwhole -f your_gro_file.gro -x your_xtc_file.xtc -sel ‘not resname WATER IONS’ -o whole.xtc

as the output will not include the solvent and ions, you will also need to run this command once to create a matching gro file (if you want to visualize).

mdvwhole -f your_gro_file.gro -x your_gro_file.gro -sel ‘not resname WATER IONS’ -o whole.gro

Please contact me if you have any issues and/or create an issue at the github page.

Cheers,

Bart