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

[David van der Spoel]

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