[gmx-users] Buckingham Potential
Mark.Abraham at anu.edu.au
Tue Aug 18 02:59:54 CEST 2009
Andrew Paluch wrote:
> 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.
Be aware that "table lookups" for non-bonded interactions refer to
tables in which GROMACS does lookups of complex functions of r for
non-bonded interactions. See various manual sections for details. I'm
not sure to what your usage of "table" refers.
> 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?
Buckingham requires the evaluation of an exponential function in r,
which is presumably noticeably more costly than
r_twelfth = r_sixth * r_sixth;
So, if you are not using table lookups, this will be considerably
slower. Even if you were using VDW table lookups, that will also be
slower than LJ.
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