AW: charm-gui membrane builder

From: Norman Geist (
Date: Mon Sep 16 2013 - 09:16:41 CDT

Hi James,


if you're using a barostat, consider increasing the relax/decay times, as
fixed atoms lead to high forces due the coordinate rescaling which moves the
non-fixed into the fixed atoms. Otherwise check your minimization log file
for messages like "Moving xxx Atoms with bad contacts downhill" or even
worse "Giving up on xxx Atoms with bad contacts". If so, you might have some
superimposed atoms in your structure. Also check if your minimization was
run for long enough by plotting the TOTAL energy and see if it converged.


Norman Geist.


Von: [] Im Auftrag
von James Starlight
Gesendet: Montag, 16. September 2013 14:08
Betreff: Fwd: namd-l: charm-gui membrane builder


Recently I've forced with new problem during simulation of the membrane

Following Namd's tutorial I've built my system consisted of receptor
embedded in the popc bilayer surrounded water and ions.

After minimization I've launch first stage of equilibration (fixed all atoms
excepts of the lipid tales)

this simulation have been crashed immediately with rattle errors.

than I've decreased timestep down to 0.3 and increased cutoffs up to 25
(because namd told me than I should do it). Within this setup I can run my
simulation but on each step I obtain

ERROR: Margin is too small for 2 atoms during timestep 5001.
ERROR: Incorrect nonbonded forces and energies may be calculated!

I have no any margin in my conf file so I have no idea how I can fix it and
what possible source of errors.

Thanks for help


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