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.
Mark
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