[gmx-users] g_sas and PBC

[Gurpreet Singh]



        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

With Regards,
Gurpreet singh

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