[gmx-users] LIE again ..

[Sandeep Somani]

Hi 

I am trying to understand the way g_lie is implemented in gmx (3.2.1).

gmx_lie.c contains:
	/* And now the great LIE formula: */
	  return fac_lj*(lj_tot-lie_lj)+fac_qq*(qq_tot-lie_qq);

So using 
	$ g_lie -f myener.edr -Elj 0  -Eqq 0 -Clj 0 -Cqq 1  -ligand
myligand 
to set fac_qq=1 , lie_lj=lie_qq=fac_lj=0 

in order to extract the total Coulombic interaction (qq_tot) of
myligand. 
This gave 
	" DGbind = -45.825 (32.233)  "
and a list of interaction terms that were used: 
	" Coul:  Coul-SR:Protein-myligand  Coul-LR:Protein-myligand  ...
etc "

now i tried to extract each of these components using g_energy expecting
the sum of average-of-each-component   would be = DGbind above but the
value i get is <1kJ !

why this disparity ? does g_lie use different energies ? 

Thanks 
Sandeep 

---
Research Associate 
Computational Biology Group
Bioinformatics Institute
Singapore 

http://www.bii.a-star.edu.sg/~ssomani