[gmx-users] How to delete atoms during MD runs?

[Yun Shi]

Hi everyone,

I am running MD of an enzyme containing co-factor FADH2.

After the enzyme stabilize, I want to reduce the FADH2 to FAD, which for me
is to delete two H atoms and change the topology file and .gro file
correspondingly.

However, I want to continue the MD run with the state (velocities,
temperature, pressure...) right before the reduction (deletion of 2 H
atoms), which requires .cpt file. How could I match the .cpt file with the
new structure that has 2 H atoms deleted?

Thanks for any suggestion or way-around,

Yun