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

[Michael Lerner]

On Sun, Jul 19, 2009 at 12:49 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> 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.
>
>>
Your last two comments there imply that rectangular boxes work. Will I get
correct results if my system has a rectangular box?

Thanks,

-michael



>
>> 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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>>
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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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-- 
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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