Re: NAMD feature request Hydrogenscale

From: Jérôme Hénin (
Date: Wed May 30 2012 - 06:51:47 CDT

Hi everyone,

While it is relatively easy to change the masses in the topology, this
may trigger unwanted behavior, as NAMD uses mass criteria to detect
hydrogen and oxygen atoms. With 4x hydrogen masses, hydrogen groups
would not be created, and water molecules would not be detected.
Correcting this would require some changes to the code, e.g. accepting
optional parameters specifying the mass of hydrogen and water oxygen


On 30 May 2012 13:16, Ajasja Ljubetič <> wrote:
>> without commenting on scientific value,
> Could we hear this comment as well? (If it is not to vulgar, of course:)
> Best regards,
> Ajasja

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