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
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