[gmx-users] INTERPRETING THE ENERGY VALUES AFTER SIMULATIONS IN GROMACS

[David van der Spoel]

On 01/04/17 06:42, Kulkarni R wrote:
> Hi gromacs users,
>
> After protein ligand simulations, I want to do energy analysis.
>
> How to interpret the following data properly? What books and papers should we refer?
>
> Energy                                   Average    Err.Est.   RMSD    Tot-Drift
> -------------------------------------------------------------------------------
> Coul-SR:Protein-MOL        -12.4549        3.6    11.7667   -19.8497  (kJ/mol)
> LJ-SR:Protein-MOL            -103.502        1.1    7.06959     6.6227  (kJ/mol)
>
> What is the significance of total drift?
>
> Can someone offer suggestions and help me to improve?
>
> Thanks,
> Kulkarni.R
>
These numbers have no real physical meaning isolated from the rest of 
the system. Please check tutorials on free energy calculation.

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se