Subject: Summary of responses for WHAM question

From: Nilesh Banavali <[email-masked]>
Date: Fri, 26 Jan 2001 17:33:18 -0500 (EST)

Hi CCLers,

 Here is a belated summary for the WHAM programs available and comments
regarding possible differences amongst them. Thanks to Jerome Baudry and
Konrad Hinsen for their help. 

Serge Crouzy and Konrad Hinsen have their own WHAM programs.

'As for possible differences in the results, I would first check the
default values for all the WHAM parameters. In particular, the number of
iterations of the WHAM equations was found to significantly affect the
convergence of the results (see following paper by Crouzy et al.). Also,
in the case of a periodic degree of freedom, like e.g. a dihedral angle,
the final results would be changed if you correct the hysteresis (by, for
instance, replicating times series at the ends of the reaction coordinate,
or by imposing equality of the PMF values at both ends of the reaction
coordinate during the WHAM iterations)' - Jerome Baudry 

'There could be minor differences due to different criteria for
terminating the iterations etc. These differences could become important
when the data is insufficient (e.g. no sufficient overlap between
neighbouring windows)' - Konrad Hinsen 

References 

Efficient calculation of 2-dimensional adiabatic and free energy maps:
Application to the isomerization of the C13=C14 and C15=N16 bonds in the
retinal of bacteriorhodopsin. Serge Crouzy, Jerome Baudry, Jeremy C. Smith
and Benoit Roux. J. Comp. Chem. 20,15 (1999) 1644-1658. 

Justin Gullingsrud, Rosemary Braun, and Klaus Schulten. Reconstructing
potentials of mean force through time series analysis of steered molecular
dynamics simulations. Journal of Computational Physics, 151:190--211,
1999. ( see this paper at: 
http://www.ks.uiuc.edu/Publications/Papers/abstract.cgi?tbcode=GULL99 ) 

O. Roche, K. Hinsen, M.J. Field Theoretical study of the conformation of
the H-protein lipoamide arm as a function of the terminal group Proteins
36(2), 228 (1999)

 Thanks,

 Nilesh Banavali
 Graduate Student,
 University of Maryland.