lie

Calculate linear interaction energy between user-specified ligand and surroundings.

lie [<name>] <Ligand mask> [<Surroundings mask>] [out <filename>][noelec] [novdw] [cutvdw <cutoff>] [cutelec <cutoff>] [diel <dielc>]

DataSet Aspects:
[EELEC] Electrostatic energy (kcal/mol).
[EVDW] van der Waals energy (kcal/mol).

For each frame, calculate the non-bonded interactions between all atoms in <Ligand mask> with all atoms in <Surroundings mask>. Electrostatic and van derWaals interactions will be calculated for all atom pairs. A separate electrostatic and van derWaals cutoff can be applied, the default is 12.0 Angstroms for both. <dielc> is an optional dielectric constant. Either the electrostatic or van derWaals calculations can be suppressed via the keywords noelec and novdw, respectively.
The electrostatic interactions are calculated according to a simple shifting function shown below.

E_{\text{elec}}=k\frac{{q_i}{q_j}}{r_{ij}} \left(1-\frac{r^2_{ij}}{r^2_{\text{cut}}}\right)

The data file will contain two data sets—one for electrostatic interactions and one for van der Waals interactions. Periodic topologies and trajectories are required (i.e., explicit solvent is necessary). The minimum image convention is followed.