Inquiry Regarding Differences in Protein Centering Behavior between Amber and GROMACS

User discussions
1

GROMACS version:2023.3
GROMACS modification: No
Dear all,

I have centered a membrane protein using both Amber (with CPPTRAJ) and GROMACS (with trjconv) tools. I observed that the centering performed by Amber appears to be better. In Amber, the protein remains stable without bouncing around, whereas in GROMACS, although the protein is centered, it exhibits slight movement in each frame.

I am curious about the difference in behavior between the two tools, considering that both center to the center of mass. Below are the commands used in both Amber and GROMACS:

Amber:

trajin prod1.nc
center :1-1310 mass origin   # There are 1310 protein residues
image origin center familiar
trajout prod1_center.nc
go
``

To run the above script:

cpptraj -i image_center.ptraj -p step5_input.parm7


**GROMACS:**

gmx trjconv -s topol.tpr -f trajectory.xtc -pbc mol -center -o centered_trajectory.xtc


Then select group 1 protein and group 4 system.

I would appreciate any insights into why there is a difference in behavior, despite both tools centering to the center of mass.

Thank you.
Pawan
2

Dear @jalemkul, any insights in above question? Any suggestions will be appreciated. Thank you.

Pawan

3

I have no insight into the cpptraj code, but it is rather magic in terms of “just working” without much user input.

4

I’m just speculating, but it’s possible that Amber either ignores hydrogens or protein sidechains when centering.

Instead of using protein as selection group with gmx trjconv you could try making a selection with only the protein backbone (or C alphas) and see if that makes it more similar to the Amber cpptraj centering.

5

I tried that but it did not solve the problem. I was interested in centering because I want to create a movie of the MD simulation without the jumps. With VMD’s RMSD trajectory tool (align to the protein backbone) and smoothing option, I was able to center the protein and see the conformation changes, and create movie. Thanks for you suggestions. Pawan

6

Thank you for the reply. ( I just discovered this message was not sent) I was interested in centering because I want to create a movie of the MD simulation without the jumps. With VMD’s RMSD trajectory tool (align to the protein backbone) and smoothing option, I was able to center the protein and see the conformation changes, and create movie. Thanks for you suggestions. Pawan