Hi,<br><br>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:<br><br> if ((ePBC != epbcXYZ) || bPBC) {<br>
fprintf(stderr,"\n\nWARNING: Analysis based on vacuum simulations (with the possibility of evaporation)\n" <br> "will certainly crash the analysis. Turning off pbc.\n\n");<br> bPBC = FALSE;<br>
}<br><br>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?<br><br> - if bPBC starts off as FALSE, it doesn't matter because the block only sets it to FALSE<br>
- if bPBC starts off as TRUE, it sets off the RHS of the ||, which ends up setting it to FALSE<br><br>I couldn't see another place where the code would set bPBC back to TRUE for my system. <br><br>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.<br>
<br><br>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.<br><br>Thanks,<br>
<br>-michael<br clear="all"><br>-- <br>Michael Lerner, Ph.D.<br>IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>
Rockville, MD 20852 (UPS/FedEx/Reality)<br>Bethesda MD 20892-9314 (USPS)<br>