[gmx-users] g_sas and PBC

[David van der Spoel]

Gurpreet Singh wrote:
>   
> 
>     Gurpreet Singh wrote:
>      > Dear Gromacs Users,
>      >
>      > I am using g_sas program of gromacs to calculate SASA, ?using
>     -pbc flag.
>      > It seems to me that the program does not take into account the
>     periodic
>      > boundary conditions.
>      > Even thought this problem is mentioned in the mailing list, it
>     still not
>      > clear whether the program can or cannot take into account the
>      > periodicity.
>      > i am using gromacs3.3.2 . Could anyone please clarify this.
>      >
> 
> 
>     http://bugzilla.gromacs.org/show_bug.cgi?id=180
> 
>     I downloaded the gromacs 3.3.3 and carried out some test
>     calculations. The PBC is still not working, at least with test i
>     have performed.
>     I generated a trajcetory file containing two atoms in a cubic box of
>     4nm having same x and y coordinates and varied the z coordinates of
>     one of the atoms.
>     one atom is fixed at z coordinate of 3.9. The result of sasa vs
>     coordinates is as follows:
>               
>     Step no        z coordinate                 total_sasa
>                1     2.05000000074506       14.1497
>                2     2.10000000149012       14.1497
>                3     2.15000000223517       14.1497
>                4     2.20000000298023       14.1497
>                5     2.25000000372529       14.1497
>                6     2.30000000447035       14.1497
>                7     2.35000000521541       14.1497
>                8     2.40000000596046       14.1497
>                9     2.45000000670552       14.1497
>               10     2.50000000745058       14.1497
>               11     2.55000000819564       14.1497
>               12     2.60000000894070       14.1497
>               13     2.65000000968575       14.1497
>               14     2.70000001043081       14.1497
>               15     2.75000001117587       14.1497
>               16     2.80000001192093       14.1497
>               17     2.85000001266599       14.1497
>               18     2.90000001341105       14.1497
>               19     2.95000001415610       14.1497
>               20     3.00000001490116       14.1497
>               21     3.05000001564622       14.1497
>               22     3.10000001639128       14.1497
>               23     3.15000001713634       14.1497
>               24     3.20000001788139       14.1497
>               25     3.25000001862645       14.1497
>               26     3.30000001937151       14.1497
>               27     3.35000002011657       13.7971
>               28     3.40000002086163       13.1359
>               29     3.45000002160668       12.5849
>               30     3.50000002235174       11.9237
>               31     3.55000002309680       11.3727
>               32     3.60000002384186       10.7115
>               33     3.65000002458692       10.1605
>               34     3.70000002533197       9.49926
>               35     3.75000002607703       8.94826
>               36     3.80000002682209       8.39726
>               37     3.85000002756715       7.51566
>               38     3.90000002831221       14.1497
>               39     3.95000002905726       7.51566
>               40    2.980232238769531E-008  14.1497
>               41    5.000003054738045E-002  14.1497
>               42    0.100000031292439       14.1497
>               43    0.150000032037497       14.1497
>               44    0.200000032782555       14.1497
>               45    0.250000033527613       14.1497
>               46    0.300000034272671       14.1497
>               47    0.350000035017729       14.1497
>               48    0.400000035762787       14.1497
>               49    0.450000036507845       14.1497
>               50    0.500000037252903       14.1497
>               51    0.550000037997961       14.1497
>               52    0.600000038743019       14.1497
>               53    0.650000039488077       14.1497
>               54    0.700000040233135       14.1497
>               55    0.750000040978193       14.1497
> 
> 
> I used the following command to calculate the sasa
> g_sas_d -f test.xtc -s topol.tpr -pbc -ndots 500
> 
> I can attached the tpr and xtc file if needed


Please reopen the bugzilla and send your input there.

> 
> With Regards,
> Gurpreet singh
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
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