[gmx-users] help(Free Energy)

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 21 20:12:40 CEST 2010

shikhar gupta wrote:
> Hi gmx users,
> I used g_lie command to compute free energy.
> The command and the output is as follow
> [shikhar at venus 30078-dyn10ns]$ g_lie -f edr.edr -ligand UNK -o lie10ns.xvg
> -ligand string UNK Name of the ligand in the energy file
> Opened edr.edr as single precision energy file
> Using the following energy terms:
> LJ: LJ-SR:Protein-UNK LJ-LR:Protein-UNK LJ-14:Protein-UNK LJ-SR:SOL-UNK 
> LJ-LR:SOL-UNK LJ-14:SOL-UNK LJ-SR:UNK-rest LJ-LR:UNK-rest LJ-14:UNK-rest
> Coul: Coul-SR:Protein-UNK Coul-14:Protein-UNK Coul-SR:SOL-UNK 
> Coul-14:SOL-UNK Coul-SR:UNK-rest Coul-14:UNK-rest
> Last frame read 50000 time 10000.000
> DGbind = -88.393 (5.098)
> gcq#306: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
> The value is coming DGbind = -88.393 (5.098).
> Whether this is correct method to get the free energy of binding of a 
> ligand.

There are numerous methods for calculating the free energy of binding, like PMF 
and thermodynamic integration.  The better question is whether or not LIE is 
accurate enough for what you want to do, and if you've done the calculations 
right.  Based on your above command, you have allowed the default values for 
-Elj and -Eqq (zero) to be used.  Are you sure this is appropriate?

In my experience, LIE is not as rigorous as the other methods I mention above, 
but I don't know anything about your system or purposes, so I'd suggest you have 
a look at the literature about LIE, its assumptions and proper usage, and go 
from there.


> Any other command or method is there to get the free energy of binding 
> of ligands or can we do the MM/PBSA and MM/GBSA analysis from the 
> gromacs dynamics.
> ------------------
> Shikhar Gupta
> Senior Research Fellow
> Pharmacoinformatics Department
> Block- A (Room No.- 208)
> National Institute of Pharmaceutical Education & Research( NIPER )
> Sec- 67, S.A.S Nagar
> Mohali, Punjab (India)
> Web-Site: www.niper.ac.in
> PIN- 160062
> Email:shik_sun at rediffmail.com,shiksun at gmail.com
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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