[gmx-users] energy minimization problem

[Kai Zhuang]

hi all,

i'm trying to minimize a rather large protein.

i tried it in water, 2 bonds won't shrink to the proper size. 
(they're both bonds of back bone carbons, should be around 1.5 in
length but shrink down to 2.45 and won't go any further)

i tried to minimize in vacuum.  set etol = 200 and used conjugate
gradient method... the same bonds still gives me problems.

am i missing anything? is there somewhere i should check?

-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789