From: James Starlight (jmsstarlight_at_gmail.com)
Date: Mon Sep 16 2013 - 07:07:43 CDT
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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