From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Apr 03 2006 - 18:15:23 CDT
Dear NAMD users,
I'm performing a MD simulation with Langevin dynamics. The damping
coefficient is set to 10 and I'm also using rigidBonds for hydrogens:
rigidBonds all
rigidIterations 500
with a timestep of 2 fs.
Is it worth and does it not affect accuracy if I use "langevinHydrogen
off"? I would think it makes sense to use "langevinHydrogen off" when
using rigidBonds because the position of the hydrogens is calculated
differently than for heavy atoms and thus it should not matter whether
hydrogens are coupled to the heat bath or not. Am I wrong?
Many thanks for your advice,
Gianluca
-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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