[gmx-users] beta hairpin; folding times; discrepancy between experiment and simulations

Xavier Periole x.periole at rug.nl
Thu Jun 16 11:03:49 CEST 2005

Y U Sasidhar wrote:

> From published papers and our own experience
> beta hairpins fold from unfolded states, like extended conformations, 
> on nanosecond time scale.
> However experimentally they are known to fold
> on microsecond time scale. 

Do you have references ?? I do not know those works where the B-hairpin
folds in nanoseconds of Brute Force MD in explicit solvent !!!!

> What is the source of this
> discrepancy ? Force field inadequacy ?

The time scale of folding for peptides is variable. It depends on the 
of course but also in the conditions the experiment is conducted. Those
conditions are not necesseraly reproductible in the simulations.

There are very few simulations that actually show an accurate description of
the folding thermodynamics of a peptide with comparison with experiment.
Again if you have references please share I am interested.


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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