[gmx-users] Positive free energy from Thermodynamics integration

[daniel madulu shadrack]

Dear All,

I am performing TI using gromacs for two system i.e receptor and ligand.
Here the receptor is a polymer i.e chitosan but I am getting + 115 +/-0.9
kJ/mol. The final results are here below and I have attached my sample
input files. Please assist, is correct to get this energy? should I assume
that the reverse reaction is negative? Or what is my problem in my input
files? I am calculating using bar module.

Temperature: 300 K

Detailed results in kT (see help for explanation):

 lam_A  lam_B      DG   +/-     s_A   +/-     s_B   +/-   stdev   +/-
     0      1    9.60  0.32    2.22  0.33    1.89  0.26    2.32  0.19
     1      2    6.24  0.15    1.47  0.18    1.34  0.17    1.83  0.10
     2      3    3.33  0.10    1.57  0.12    1.40  0.11    1.83  0.08
     3      4    0.83  0.11    1.09  0.04    1.04  0.04    1.50  0.03
     4      5    2.73  0.04    0.25  0.08    0.31  0.10    0.64  0.03
     5      6    2.67  0.06    0.06  0.07    0.08  0.07    0.58  0.01
     6      7    5.49  0.03    0.57  0.04    0.80  0.03    1.16  0.01
     7      8    5.34  0.07    0.64  0.06    0.90  0.07    1.23  0.03
     8      9    5.12  0.06    0.70  0.07    0.99  0.17    1.45  0.04
     9     10    4.62  0.07    1.11  0.12    1.52  0.10    1.58  0.06
    10     11    4.07  0.12    0.98  0.04    1.46  0.09    1.72  0.03
    11     12    1.73  0.04    0.49  0.04    0.55  0.03    0.93  0.01
    12     13    1.52  0.08    0.37  0.05    0.49  0.06    0.99  0.02
    13     14    1.10  0.10    0.67  0.06    0.92  0.08    1.25  0.04
    14     15   -0.30  0.13    1.47  0.14    2.13  0.20    1.98  0.11
    15     16   -2.67  0.18    1.78  0.14    1.66  0.14    2.04  0.10
    16     17   -2.89  0.06    0.53  0.08    0.43  0.04    0.99  0.04
    17     18   -1.77  0.01    0.18  0.01    0.17  0.01    0.57  0.01
    18     19   -0.57  0.01    0.08  0.01    0.09  0.01    0.42  0.01


Final results in kJ/mol:

point      0 -      1,   DG 23.94 +/-  0.80
point      1 -      2,   DG 15.56 +/-  0.37
point      2 -      3,   DG  8.29 +/-  0.24
point      3 -      4,   DG  2.07 +/-  0.28
point      4 -      5,   DG  6.82 +/-  0.11
point      5 -      6,   DG  6.66 +/-  0.14
point      6 -      7,   DG 13.69 +/-  0.07
point      7 -      8,   DG 13.32 +/-  0.18
point      8 -      9,   DG 12.78 +/-  0.14
point      9 -     10,   DG 11.53 +/-  0.16
point     10 -     11,   DG 10.15 +/-  0.30
point     11 -     12,   DG  4.33 +/-  0.11
point     12 -     13,   DG  3.79 +/-  0.20
point     13 -     14,   DG  2.74 +/-  0.24
point     14 -     15,   DG -0.74 +/-  0.32
point     15 -     16,   DG -6.65 +/-  0.45
point     16 -     17,   DG -7.22 +/-  0.15
point     17 -     18,   DG -4.42 +/-  0.02
point     18 -     19,   DG -1.42 +/-  0.02

total      0 -     19,   DG 115.21 +/-  0.94


gcq#404: "Humbug! Most things free-born will submit to anything for a
salary" (Mr. Rochester in Jane Eyre by Charlotte Bronte)

Thank you for your help

-- 


*Regards,               *
Daniel Madulu Shadrack., (M.Sc. Chem).
PhD Research Scholar
(Nanomedicine & Comp. Aided Drug Design)

  dmssjut at gmail.com
-
*FOR GOD LET US DO MUCH, **QUICK AND **WELL*..
                                          *St. Gaspar Del Bufalo*