Steered MD pulling rate does not result in desired final pulling distance

User discussions
1

GROMACS version: 2019.4
GROMACS modification: No

Hello,
I have been running some steered MD pulling simulations on a receptor-ligand complex. I decided to pull the ligand out of the active site of the receptor for a total distance of 2.5 nm (the distance is being measured between a reference atom of the protein and an atom of the ligand).

I am pulling the ligand in two different directions. For each direction, the pulling rate is 0.005 nm/ps and the pulling force is 1000 kcal/mol. The length of the simulations is 500 ps. Thus, the total distance that the ligand should be pulled out of the active site is 0.005 nm/ps x 500 ps = 2.5 nm.

However, this only happens for one of the pulling directions and not for the other. For the other, the ligand is only pulled 0.89 nm. All the pull code settings for both pulling directions are the same. The only difference of course is the direction of the pulling.

I increased the length of the simulation to 1 ns and when I looked at it, the ligand reaches the 2.5 nm distance after ~850 ps. Does anyone have any idea why this is happening?

I could just simply use the longer simulation for my analysis but I thought that the pulling rate should determine the pulling distance, and because it seems that this is not the case here, I want to make sure that it is okay to use the longer simulation and that this is not an issue that needs fixing in some other way.

Best wishes,
Pawel

2

The pull rate defines how fast the virtual spring extends, but the response of the system is governed by the restoring forces that the molecules experience. Thus you cannot directly compute the displacement from the input parameters.

3

Many thanks for the reply. I understand this now.

Best wishes,
Pawel