[gmx-users] best structure

UCT Staff Member - Jackson Jackson at SCIENCE.uct.ac.za
Wed Feb 9 08:08:53 CET 2005

Dear Users
I have done a restrained molecular dynamics of a cyclic peptide in a
biphasic solvent box.  I have used different starting conformations and
collected 100 structures during each run.  After cluster analysis I get
3 clusters.  How do I tell which is the 'best' structure.  If I was
working in vacuum I could use the potential energy as a criterion but I
am working in solution.  I have tried using restraint violations, both
in terms of the number of violations and their magnitude.

In theory I could start the simulation with all cis peptide bonds.  The
energy would be very high but at 300K I would not get cis-trans
isomerization.  Hence I could end up with energetically unrealistic
structures as long as they did not violate my restraints.

In essence the difficulty is to compare the energy of different
simulations on different conformations of the same molecule but in a
solvent box of slightly different size and number of solvent molecules.

Any help

Professor Graham E. Jackson
Department of Chemistry
University of Cape Town

Tel: (021) 6502531
Fax: (021) 6897499

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