[gmx-users] energy minimization in charged systems
bhadaur1 at illinois.edu
Thu Apr 8 07:11:20 CEST 2010
I am trying to simulate a electroosmotic flow in a nanochannel. System
consists of water + (Cl-) ions in a channel confined of silicon <111> walls.
I start with taking water as only solvent, equilibrating the system for
about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-)
ions. Walls are charged appropriately to maintain electro-neutrality in the
system. The problem is with Energy minimization after inserting ions using
steep algorithm (haven't turned on the electric field yet). I am getting an
error like this:
t = 0.038 ps: Water molecule starting at atom 2569 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Steepest Descents converged to machine precision in 88 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.75456106043895e+06
Maximum force = 1.07111309902475e+11 on atom 4898
Norm of force = 1.48772609239112e+09
If it were only couple of such molecules, I could have removed them easily
from the gro file. The problem is twofold, there are around 10 molecules
which give this error message, plus even after removal of these molecules,
energy minimization results in the same error on different sets of
molecules. I have tried a number of ways to tackle this including tuning the
time step. Is there any way to avoid this? Any help would be appreciated.
Thanks in advance.
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