[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
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--
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
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