[gmx-users] Positive free energy from Thermodynamics integration
Billy Williams-Noonan
billy.williams-noonan at monash.edu
Mon Apr 1 10:00:43 CEST 2019
Hey Daniel,
Is this an absolute or relative perturbation? In either case you need to
do the same transformation in water (over however many lambda states) and
close the thermodynamic cycle. Have you got those results?
Cheers,
Billy
On Mon, 1 Apr 2019 at 18:09, daniel madulu shadrack <dmssjut at gmail.com>
wrote:
> 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*
> --
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--
Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
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