Tutorial-l Mailing List

From: Ribi Akbar (ra.ribiakbar_at_gmail.com)
Date: Mon May 16 2022 - 08:27:54 CDT

Hi,

I am trying to follow this tutorial: *Methods for calculating Potentials of
Mean Force*

I do understand how to specify the distance for each window for the colvar,
but on page 11, there is this statement "*Using the trajectory from the SMD
simulation, find frames in which NH3 is somewhere in each of the windows,
i.e., between 2 and 7 ˚ A above the protein’s center of mass and so on.
Write out a PDB for the entire system for each representative frame named,
e.g., win1start.pdb. These will be the starting points for the four
individual ABF simulations"*

My question is how to obtain the pdb file for each window?

*find frames in which NH3 is somewhere in each of the windows*
At this point, NH3 is always somewhere during the course of the
trajectories, but are there any specific points such that we could define
the correct position of NH3 for each window?
should we play the trajectories and write the PDB file at that point?

I would look forward to your kind reply.

Best regards,
Ribi

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