APBS requires approximately 200 B memory per grid point. Memory usage can be predicted before performing the calculations using the
If it appears your calculation is going to require more memory than is currently available on your system, you have a few options:
The actin dimer example provided with the APBS distribution (examples/actin-dimer/complex.pqr) is a fairly large system that can often require too much memory for some systems. As such, it is a good example for parallel focusing calculations. This example will use the actin dimer complex PQR file complex.pqr.
We're going to use an 8-processor parallel calculation to write out the electrostatic potential map for this complex. Each processor will solve a portion of the overall problem using the parallel focusing method on a 973 mesh with 20% overlap between meshes for neighboring processors. An example input file for this calculation might look like:
Running this input file with an MPI-compiled version of APBS runs 8 parallel focusing calculations, with each calculation generating fine-scale solutions on a different region of the (
However, most users are interested in global potentials. For some programs (OpenDX, DataTank), the individual potential files can simply be read into the program separately and the program will reconstruct the global map. Most other programs will require the user to reassemble the global map first; APBS provides the
will generate a file
The steps described in the previous section can also be performed for systems or binaries which are not equipped for parallel calculations via MPI. In particular, you can add
to the ELEC mg-para section of the APBS input file to make the single-processor calculation masquerade as processor n of a parallel calculation.
Scalar maps from asynchronous APBS calculations can be combined using the
As a specific example, we can modify the input file above to include an async 0 command in the ELEC statement and thus cause APBS to perform the operations of the first processor in the parallel focusing calculation. The modified input file should look like:
This should create an OpenDX-format potential map called pot.dx, corresponding to the output from processor 0 in a parallel focusing calculation. Performing additional APBS calculations with