From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Fri Feb 02 2007 - 07:31:53 CST
I am using VMD's membrane plugin to construct a membrane, solvating it,
and then trying to equilibrate it. The membrane generated by VMD does have
a lot of bad contacts, but I thought NAMD would handle them.
I keep getting the "atoms moving too fast" error as soon as I start
heating the bilayer after minimzation. I have tried the following, but
nothing works so far:
- heating in very small increments (~ 3 degrees every 3000 steps)
- larger cutoffs (16 A)
- with/without constraints on head groups
- larger box sizes (than suggested by the minmax of water)
Any suggestions into what might be going wrong ? The config file is
attached with this email,
Thank you !
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