[gmx-users] energy minimization for a normal mode analysis

Kristina Woods kristina.woods at gmail.com
Fri Jul 8 18:40:09 CEST 2005


I am trying to minimize a fragment of DNA in solvent (water and
counterions) using conjugate gradient minimization for a normal mode

Looking at the questions regarding this topic from the archived list
it seems like for the minimization step all cut-offs should = 0 and
pbc should be turned off.  Is this  just the case for a system in
vacuum?  If so, does anyone have any suggestions for a system that is
not in vacuum?

Thank you,

Kristina :)

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