[gmx-users] pulling time

[Alexander Alexander]

Dear gromacs user,

I was wondering how long normally should be the pulling time in one step
before the final umbrella sampling?
For instance in the Aβ42 protofibril umbrella sampling used in tutorial,
the applied simulation times are as following referring to the original
paper:

Production Normal MD: 100 ns
Pulling time :  500 ps
MD in each windows : 10 ns


The second question is that can we limit the pulling region to pull away
for example A from B as 3 nm in the pulling run(not in the final umbrella
sampling)?

Thanks,
Regards,
Alex