[gmx-users] Trying to use g_sas with pbc, also trying to get per-frame output.

Michael Lerner mglerner+gromacs at gmail.com
Sun Jul 19 18:30:34 CEST 2009


I'm trying to use g_sas on a membrane system. It keeps complaining that all
of my simulations are done in vacuum (they're not). I poked through
gmx_sas.c and found this block:

  if ((ePBC != epbcXYZ) || bPBC) {
   fprintf(stderr,"\n\nWARNING: Analysis based on vacuum simulations (with
the possibility of evaporation)\n"
        "will certainly crash the analysis. Turning off pbc.\n\n");
    bPBC = FALSE;

It's been a while since I did anything in C (Python rots the brain
apparently), but doesn't that block always end up setting bPBC to FALSE?

 - if bPBC starts off as FALSE, it doesn't matter because the block only
sets it to FALSE
 - if bPBC starts off as TRUE, it sets off the RHS of the ||, which ends up
setting it to FALSE

I couldn't see another place where the code would set bPBC back to TRUE for
my system.

When I change that initial if to say "if (ePBC != epbcXYZ) {", I get
reasonable looking answers, but I want to make sure that I'm not opening up
some weird bug.

The other question I had was whether it was possible to get g_sas to write
its output files on a per-frame basis. That is, I'd like resarea_1.xvg for
frame 1, resarea_2.xvg for frame 2, etc.



Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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