[gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation

[Mark Abraham]

On 5/01/2011 5:06 PM, devawati dutta wrote:
> Dear Sir,
>               I am using Gromacs 3.3.2 version for molecular dynamics 
> simulation of my protein-ligand complex. I want to calculate the free 
> energy of binding through LIE method. While extracting the LJ and 
> coulombic energy values using g_energy command,there are many options 
> like LJ-14, LJ-SR, LJ-LR, Coul-14, Coul-SR, Coul-recip etc. I am 
> unable to decide which values should I use for free energy 
> calculation .Which of the following options should I consider.
> 1. Should I use only LJ-SR and coul-SR?
> 2. Should I use the total energy values i.e LJ-SR+LJ-LR?

LIE does not work with PME. This issue has been discussed on this list 
many times, if you search the list archives.

Also, unless you need continuity with earlier work, you should upgrade 
to the latest GROMACS for much better performance and fewer bugs.

Mark