From: Mahya Hemmat (hemma011_at_umn.edu)
Date: Mon Jul 06 2015 - 11:06:39 CDT
Hi all NAMD users,
I'm trying to do SMD via NAMD, pulling one protein dimer away from another
dimer. However, when I fix some of the atoms of the static dimer, and try
to pull the other dimer away with constant velocity, I face the Error below:
Constraint failure in RATTLE algorithm for atom 5380!
(each time for a different atom)
I initially minimized my system for 4000 timesteps and then increased the
minimization steps to 10000 and then let the system be in equilibrium for
0.1 ns, but the problem still shows up when trying to do SMD.
My time step is set to 1 fs which is small enough.
It is notable that the simulation runs without error when none of the atoms
are fixed and no constraint is applied to smd atoms. but in that case, the
first dimer will follow the second dimer which is pulled.
Can anyone gives a hint which might be wrong in fixing the atoms?
Thanks for your help.
-- Mahya Hemmat PhD Student Department of Mechanical Engineering University of Minnesota Minneapolis, MN 55455 USA Email: hemma011_at_umn.edu
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