[gmx-users] best structure

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 9 08:13:43 CET 2005


On Wed, 2005-02-09 at 09:08 +0200, UCT Staff Member - Jackson wrote:
> 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.
If you've sampled sufficiently, then the most populated cluster is the
best one. Of course it can be tricky with cis/trans isomerization.

> 
> 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
> 
> Grahan
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++





More information about the gromacs.org_gmx-users mailing list