AMBER Archive (2002)

Subject: gibbs

From: sara nunez (mbdtssn_at_hotmail.com)
Date: Wed Aug 28 2002 - 14:52:56 CDT

Hello again,

I am still trying to run gibbs on my enzyme to get free energies for a
proton transfer.

I edited, saved the perturb and non-pertub parameters, did some minimisation
to get rid of bad contacts, also did some equilibration.

(Since my system has near 40000 atoms, I had to recompile gibbs with a
bigger parameter in gib.f file)

And finally started gibbs.

My problem now is that gibbs gives me huuuuge electrostatic energies, all
throughout the simulation. I don't know where I have gone wrong since all
the previous steps seem to have succeeded.

I am also not sure of the validity of my simulation.
Is there a way to trace down where I did wrong?

Thank you
sara

Sara Nunez
Theoretical & Computational Chemistry Group
University of Manchester
Manchester, M13 9PL
United Kingdom

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