From: Low Soo Mei (lowsm_at_bii.a-star.edu.sg)
Date: Fri Mar 14 2008 - 04:57:27 CDT
Dear NAMD users,
The question has been asked before, here,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3693.html , but
I could not find a reply on the mailing list. I wonder if someone with
better physics than me could help :)
My timestep is 2 fs and I am using Langevin dynamics, NVT for early
equilibration and NPT for the later part of equilibration and also the
actual runs. For a 2 fs timestep, I read that rigidBonds "all" is
recommended, to freeze all hydrogen-related bond lengths and bond
angles. Under these conditions, does it necessarily follow that
langevinHydrogen must be "off"?
From what little I understand of Langevin dynamics, it controls the
temperature and pressure by introducing frictional damping force and
random forces on each particle in the system. So, langevinHydrogen
"off" means that these friction and random forces are not applied to the
H atoms, but yet the H atoms will still be able to move according to the
forces on other atoms? Even though the hydrogen-linked bonds have been
'frozen' by rigidBonds.
Thanks for your advice in advance, and I am most grateful. References
for additional (basic) reading are welcome as well.
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