[gmx-users] Trying to use g_sas with pbc, also trying to get per-frame output.
David van der Spoel
spoel at xray.bmc.uu.se
Sun Jul 19 18:49:13 CEST 2009
Michael Lerner wrote:
> Hi,
>
> 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;
> }
There is an open bugzilla about this. That means the code will not work
reliably with PBC.
>
> 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.
>
> Thanks,
>
> -michael
>
> --
> 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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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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