NAMD feature request Hydrogenscale

From: Norman Geist (
Date: Wed May 30 2012 - 02:36:16 CDT

Hi Guys,


I would like to do this feature request about a possibility to scale up the
mass of hydrogen atoms within a simulation to be able to use larger
timesteps with NAMD. As I think, many people need large simulation times for
their systems like protein folding etc. The easiest way to increase this
simulation time without much loss in computing time, precision and money, is
to increase the timestep, if one is not looking for to fine grained
mechanisms. Other simulation software like ACEMD provide such a parameter
and make it possible to use a stable timestep of 4 fs while is scales up the
hydrogens to the 4x mass and reducing the mass of the "mother atom" by the
same amount, so that the total mass is constant.


If I try to use such a large timestep with NAMD, I cannot get around this
rattle constraint errors.


I would like you to share your opinions with me.


Best wishes


Norman Geist

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