<br><br><div class="gmail_quote">On Sun, Jul 19, 2009 at 12:49 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Michael Lerner wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
There is an open bugzilla about this. That means the code will not work reliably with PBC.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
</div></blockquote></blockquote><div><br>Your last two comments there imply that rectangular boxes work. Will I get correct results if my system has a rectangular box?<br><br>Thanks,<br><br>-michael<br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><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>
<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>
<br>
<br></div>
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</blockquote>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</blockquote></div><br><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>