[Apbs-users] Can APBS write out a smaller pot.dx file?

[Daniel E. <de...@ma...>]

Hi,

The thought has crossed my mind that I may be crazy, but:
- I have 6,036 frames from molecular simulation for which I would like
  to calculate the potential
- Using the gz option of the "write" keyword, I get 11 MB pot.dx.gz
  files
- I'm not confident in my focusing strategy and my grid spacing, so I'm
  trying 2 focusing strategies and 4 different grid spacings
- That's 8 * 6,036 * 11 MB * 1 GB / (1024 MB) = 518 GB total data.
  Yikes.

At this point I don't *need* all that data, I just need the electric
field at ~11 points along a particular bond in each MD snapshot. Right
now I'm using the vgrid library in Python to calculate this, then
throwing away the dx files. However, this is contributing to a
difficult time debugging, and I was wondering if APBS can just give me
the potential either

1. just at the points I want, or
2. just a portion of the final potential map. In other words, right
now get the 19 A-cube grid, but can I get, say, just the central 3
A-cube grid output instead?

I've considered modifying the code myself to do this; it looks like I
could add options to the input file by modifying src/generic/pbeparm.c
and src/generic/apbs/pbeparm.h, and write out what I want in main()
somewhere near the call to writedataMG() using a call to the vgrid
routines?

Thanks for any help,
Dan


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