[gmx-users] Problem with Umbrella Sampling simulation

[Daniele Veclani]

Dear Gromacs Users

I'm trying to calculate the potential mean force between two molecules (A
and B).

I created the various configurations through the pull simulation. To do
this I kept fixes the position of the molecule A (position restraint)

I have extracted the coordinates and sampled the various configurations.

Now I have to use these configurations as input for umbrella sampling
simulation.

I have a couple of questions:

- Do I have to maintain a position restraint on A molecule?

- Do I have to enter the position restraint even for molecule B? (Otherwise
during the dynamic simulation I a change of the distance between molecule A
and B)

- Can I get a clear explanation about this last step of the job?

Best regards,
D.V.