[gmx-users] Positive free energy from Thermodynamics integration
Billy Williams-Noonan
billy.williams-noonan at monash.edu
Mon Apr 1 10:04:54 CEST 2019
Also, just a side note. If you are using *gmx bar*, then you are not doing
TI, you are using BAR :-)
FEP was originally derived by Zwanzig (1954). There are different
mathematical derivations of FEP, such as TI, BAR, etc :-) Gromacs has
built in code for doing a BAR calculation. If you want to use TI
specifically (it shouldn't really make much difference) then look through
github for alchemical_analysis.py
Cheers,
Billy
On Mon, 1 Apr 2019 at 19:00, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:
> 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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>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
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>
>
--
Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|* +61420 382 557
Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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