[gmx-users] Buckingham Potential

Andrew Paluch apaluch at nd.edu
Mon Aug 17 17:53:07 CEST 2009

To whom this may concern,

I am performing simulations for a system that is modeled with a  
Buckingham potential and PME for the electrostatic interactions.  I  
have developed my forcefield file such that non-bonded cross terms  
are listed in a table, and also 1-4 interactions are listed in a  
table with an LJ type of potential.

On 16 processors, I am able to run my system for 0.5ns in a day.  If  
I map the potential to an LJ, I am able to achieve 2.5ns in a day.   
Does anyone have any idea as to where my performance loss may be  
occurring?   Are there any special compilation or run-time flags that  
I should be using?

Thank you,


Andrew Paluch
Department of Chemical and Biomolecular Engineering
University of Notre Dame du Lac
apaluch at nd.edu

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