[gmx-developers] Problems with artificial minima when using soft-core potentials

Alan E. Mark a.e.mark at uq.edu.au
Tue Sep 4 03:01:23 CEST 2012

All of this comes down to choice and whether as developers we want to to 
provide flexibility or try to prevent users doing something which may 
cause their simulations to fail.

Enforcing the use of a single parameter for both the LJ and 
electrostatics prevented some people from making a bad choice. At the 
same time it removed the flexibility inherent in the original algorithm 
leading to the need for the various work arounds outlined.

In regard to Michael's and Bert's comments, as the alpha parameter for 
the electrostatics becomes large the algorithm effectively becomes 
equivalent to switching off the electrostatics first and thus these 
minima disappear. My concern Bert with your approach is simply that is 
that it is more complex than is needed and, as the interaction is 
reduced, that it may become possible to sample the discontinuity at r=0.


This message was composed using voice recognition software. Please forgive any strange words I fail to correct.
Prof. Alan E. Mark

Molecular Dynamics Group
School of Chemistry and Molecular Biosciences (SCMB)
University of Queensland
Brisbane, QLD 4072,


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