Problem regarding the Pre-Minimizer Bad Contacts Removal

From: Norman Geist (
Date: Wed Nov 27 2013 - 02:24:28 CST

Dear experts,


I noticed some weird/annoying problem while trying to minimize between "run"
commands to remove the velocities and potential energy saved in the
structure. It seems that a structure coming out of a temperature about 300K
looks like a really bad structure to the minimize or its preceding bad
contacts remover (about 1300 atoms with bad contacts which is almost all),
what causes NAMD to create a VDW energy of 99999999 right after the 1st step
of this bad contacts removal. The mintinystep and minbabystep doesn't seem
to affect this behavior at all. Is there a way to disable this bad contacts
removal or do you have any other suggestion?


Thank you


Norman Geist

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