MDFF - should hydrogens be included?

From: Geoffrey Kwai Wai Kong (
Date: Mon Mar 04 2013 - 00:19:26 CST

Dear all,

It is my first post in NAMD-L and I have recently started running
MDFF. I found that MDFF would run properly for my protein if the
occupancy of hydrogen atoms is set to zero (unintentionally) and I ran
a minimisation with velocity quenching before the main MDFF
simulation. But when I have the occupancy of hydrogen atoms set to
one, MDFF has never worked with or without minimisation beforehand.
The main problem is atoms with excessive velocity. So I would like to
know if setting hydrogen occupancy to zero is an appropriate thing to
do in MDFF.

(What I have in mind is something similar to the 'riding hydrogen'
model used in some crystallography refinement, whereby hydrogen atoms
are included in the model but their positions are not refined
independently of the atoms to which they are bonded.)

Thanks for your help!

Geoffrey Kong

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