Wrapping Inquiry

User discussions
1

GROMACS version: 2023
GROMACS modification: Yes/No

Hello Gromacs users,

I have a system which is an aptamer binds to AMP and run for 10us. Since the aptamer is moving inside the PBC a lot, so I tried to wrap it with these commands:

· gmx make_ndx -f 5x0x_100.tpr -o 5x0x_index_fixed.ndx

# Combine RNA (1) + AMP (12) → group 11 RNA_AMP

nojump

gmx trjconv -s 5x0x_100.tpr -f 5x0x_100.xtc -o traj_nojump.xtc -n 5x0x_index_fixed.ndx -pbc nojump
output: 0 (System)

# whole

gmx trjconv -s 5x0x_100.tpr -f traj_nojump.xtc -o traj_whole.xtc -n 5x0x_index_fixed.ndx -pbc whole

output: 0 (System)

# center + compact

gmx trjconv -s 5x0x_100.tpr -f traj_whole.xtc -o traj_center.xtc -n 5x0x_index_fixed.ndx -center -pbc mol -ur compact

center: 18 (RNA_AMP)
output: 0 (System)

# fit

gmx trjconv -s 5x0x_100.tpr -f traj_center.xtc -o traj_fit.xtc -n 5x0x_index_fixed.ndx -fit rot+trans

fit reference: 18 (RNA_AMP)

output: 0 (System)

Unfortunately, after I fit the trajectory with -fit rot+trans and visualize it in VMD, the PBC box is moving around the aptamer, so when I use +x and -x for PBC, it does not align. Could you please help me how should I wrap my system?

2

Hi @quantang1903

If I understand correctly you want to take a look at the PBC images after the full PBC clean-up procedure.

I think there is no way around this. Or you stop before the -fit rot+trans step, so you stay in the box reference frame, and so you can correctly represent the PBC images of your molecules, or you fit to a frame, and so you “move” your reference frame to the molecule, but in that case the box itself will rotate around the fitted molecule, and so will the PBC images. I would honestly visualize the trajectory before the fitting procedure if I wanted to check PBC and after if I wanted to check the molecule behaviour.

3

Hi obZehn,

Thank you so much for your suggestion. I stopped at the step before -fit rot+trans, and the PBC stopped moving, which is exactly what I want. However, I am not sure whether I need to include the -fit step, because if I stop at the center+compact step, the RNA moves more than when I include -fit as the box is moving along the RNA.

Quan