[gmx-users] Freezing Algorithm

Reza Salari resal81 at yahoo.com
Thu Oct 15 18:13:24 CEST 2009

Hi all,

I've got a question regarding freezing algorithm in
GROMACS. I appreciate it if somebody explains this.

I think in GROMACS 3 for freeze option to work it was
generally suggested that all the interactions inside the frozen part
should be excluded (either in top or mdp files). However it seems that
freeze option works in GROMACS 4 without using any explicit kind of
energy exclusions. I am curious to know that if the freezing algorithm
has been changed in version 4 to work without exclusions or at the
other hand it automatically excludes the interactions in the frozen

Thanks in advance,
Reza Salari
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