[gmx-users] Vacum minimizations and references

Xavier Periole periole at inka.mssm.edu
Wed Nov 20 19:15:53 CET 2002

Would be smart to use the "vacuum" force field of GROMACS. If I
remember it's called ffG43b1. It uses neutralized side chains for
charged residues. It avoid collapses of charges.

For dynamics in vacuum, we just sent a paper where we show that
the core of the protein is quite preserved, even though I would not
consider it reliable, but the loops collapse, even with the use of the
charge neutralized force field (comparable to a 2-4 epsilon). The
simulations where compared to a full water/bilayer/protein (rhodopsin)
simulation where nothing like that happens.

Basically be careful


Xavier Periole
Mt. Sinai School of medicine
Dpt. Physiology and Biophysics.
New York 

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