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g_lieMain Table of Contents |
VERSION 4.6.7
Fri 29 Aug 2014
| VERSION 4.6.7 |
g_lie computes a free energy estimate based on an energy analysis from nonbonded energies. One needs an energy file with the following components: Coul-(A-B) LJ-SR (A-B) etc.
To utilize g_lie correctly, two simulations are required: one with the molecule of interest bound to its receptor and one with the molecule in water. Both need to utilize energygrps such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr file. Values from the molecule-in-water simulation are necessary for supplying suitable values for -Elj and -Eqq.
| option | filename | type | description |
|---|---|---|---|
| -f | ener.edr | Input | Energy file |
| -o | lie.xvg | Output | xvgr/xmgr file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]version | bool | no | Print version info and quit |
| -nice | int | 19 | Set the nicelevel |
| -b | time | 0 | First frame (ps) to read from trajectory |
| -e | time | 0 | Last frame (ps) to read from trajectory |
| -dt | time | 0 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output .xvg, .xpm, .eps and .pdb files |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -Elj | real | 0 | Lennard-Jones interaction between ligand and solvent |
| -Eqq | real | 0 | Coulomb interaction between ligand and solvent |
| -Clj | real | 0.181 | Factor in the LIE equation for Lennard-Jones component of energy |
| -Cqq | real | 0.5 | Factor in the LIE equation for Coulomb component of energy |
| -ligand | string | none | Name of the ligand in the energy file |