g_lie computation results in 0 (or other obviosly wrong value depending on settings)
$ g_lie -f md.edr -o lie.xvg -ligand SUA
In case I set options -Eqq -Cqq -Elj -Clj result is -(Eqq*Cqq+Elj*Clj) and again data in *.edr file is clearly ignored.
I provide my edr file too.
Improvements to the g_lie help description.
Information was sparse, likely to avoid restating published
protocols, but some expansion was definitely warranted,
given the amount of questions that have recently been
posted to the mailing list and Redmine.
#3 Updated by Justin Lemkul almost 6 years ago
- Status changed from New to Rejected
This is not a bug; you're simply not executing the calculations correctly. For LIE, you need the ligand and receptor as separate energygrps in the .mdp file to get the nonbonded interaction energies between the two. Your md.edr file does not have the correct terms. You then need to simulate the ligand in water to get the water-ligand interaction energies and supply them on the g_lie command line. Since you haven't done that, the command produces nothing useful. Wrong input, wrong output.
#7 Updated by Justin Lemkul almost 6 years ago
I will check in a more detailed description for g_lie. The existing (minimal) help description assumes the user is familiar with existing LIE methods, which are reviewed extensively elsewhere. I can understand the original intent of not wanting to duplicate information, but a bit of expansion can't hurt.