Hi,
On Jun 29, 2006, at 4:41 PM, Justin M. Shorb wrote:
Erik and Mark: Thanks for your help, I will begin diving into the
code today.
Mark, if everything went ideally (which things don't always), I
would use the force tables to compute the total SR electrostatic
force on each atom in a specific group (around 2 to 7 atoms). The
same goal can be accomplished by running a trajectory and then
rerunning it to calculate the electrostatic forces exclusively.
This is what we have done before, but saving the necessary
trajectory file for our current system has gotten too costly.
Instead, I am hoping to collect the forces and save those
exclusively at each timestep (along with positions at larger
intervals). So far it has seemed that Gromacs creates a separate
coulombic and LJ table, but uses a combined table to actually
compute the forces. So it should be capable of computing the simple
ES force on the fly and saving them. Any suggestions on a better
tactic?
The separate/combined table is an optimization to improve cache
efficiency. The memory latency can be pretty significant for table
lookups (and you do billions of them in the kernels...), so by
interleaving coulomb and LJ tables the LJ part will already be in
level1 cache after doing the coulomb table interaction.
So, for all atoms that have both tabulated coulomb and tabulated LJ
interactions we use the combined table, otherwise separate (since
those are smaller).
Cheers,
Erik
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