regarding umbrella sampling simulation

From: san kumar (ksan93259_at_gmail.com)
Date: Fri Sep 14 2018 - 23:11:54 CDT

Dear NAMD users,

I am relatively new in molecular simulation field. I am using NAMD umbrella
sampling tutorial to set up umbrella sampling simulation of my protein
using NAMD. I solvated each window such that there was a minimum distance
of 13 Å between any protein atom and a box side in all directions. The
total number of water molecules in all windows is not the same. The total
number of atoms in most of the windows is ~100,000 and in some windows, it
is ~80,000.

So, is it necessary to solvate each window using same size of water box?

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,
San

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