[gmx-users] Problem with Umbrella Sampling simulation

Daniele Veclani danieleveclani at gmail.com
Fri Jul 22 14:19:27 CEST 2016


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.


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