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

Alan E. Mark a.e.mark at uq.edu.au
Mon Sep 3 17:08:34 CEST 2012

Dear Berk,
             This has been coming up in various circumstances for a long 
time.  Bert de Groot recently however published a paper in JCTC 
highlighting the problem in GROMACS and proposing a complex solution 
which in fact makes the potential have a discontinuity at r=0. This also 
makes the dynamics potentially unstable. Stable dynamics was exactly why 
the soft-core was introduced in this form in the first place.  He claims 
there is a problem with our soft-core when in reality the problem is in 
the form implemented in GROMACS which is a pity.  I would also note 
that  by being able to scale the alpha parameters for the LJ and 
electrostatics separately (i.e. using a larger shifting distance for the 
electrostatics) avoids any need to turn off the electrostatics first. 
Turning the electrostatics off completely first can add the the range of 
non-physical states that need to be sampled making the calculations 
slower and more complex than necessary.

Alpesh and I are writing a response to Bert's paper and a few other 
factors. I will send you a copy when we have a good draft.


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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