[gmx-users] re: need help with free energy of solvation calcu lation

[Moore, Jonathan (J)]

David M.,

Thanks for the suggestions.  About the Yu et al. error bars:

> For Yu et 
> al., the first number is the average from the full 5 ns simulation and 
> the number in () is for the last 2 ns.

If not for the CE23Me case, I would probably assume that the discrepancy due to doing a notoriously difficult type of calculation with different methods.  Considering CE23Me, that still may be the case but it has me more concerned.

>
> Here is the comparison:
>
> 2,3,6-methylcellononaose
> =============================
> JDM-Run1        487 ± 130 kJ/mol
> JDM-Run2        463 ± 26 kJ/mol
> Yu et al.       393 (329) kJ/mol
>
> CE236Me
> =============================
> JDM-Run1        113 ± 39 kJ/mol
> JDM-Run2        121 ± 15 kJ/mol
> Yu et al.       224 (165) kJ/mol
>
> CE23Me
> =============================
> JDM-Run1        -3.4 ± 23 kJ/mol
> JDM-Run2        16 ± 16 kJ/mol
> JDM-Run3        19 ± 10 kJ/mol
> Yu et al.       136 (136) kJ/mol
>
> CE6Me
> =============================
> JDM-Run1        70 ± 15 kJ/mol
> JDM-Run2        79 ± 9 kJ/mol
> Yu et al.       68 (50) kJ/mol

Thanks,
Jonathan

____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
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