Re: " the error of hydrogen group size "

From: Brian Radak (
Date: Wed May 01 2019 - 08:51:08 CDT

This sounds like a problem inherent to your PSF. How did you construct it?
Did you use any nonstandard residue definitions? Can you visualize the
system in VMD?

Hydrogen groups are the base unit for domain decomposition in NAMD. They
are determined almost exclusively by bond connectivity and this is usually
where issues arise.


On Tue, Apr 30, 2019, 5:28 AM soroush ziaei <>

> hi NAMD users,
> I encountered an error at the beginning of the simulation, which related
> to Atom 3662,
> please let me know the solution of this error:
> FATAL ERROR: Atom 3662 has bad hydrogen group size. Check for duplicate
> bonds...
> by the way, I didn't find a duplicate bond in the parameter file and I
> want to know, what's the meaning of hydrogen group size?
> is it possible to know the root of this message?

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