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

[Kristina Woods]

Hello:

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

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 :)