Using the "old" AMBER (prep/link/edit/parm), the state defined in PREP is the state and the state given in the PARM is the state. Using LEaP, the default state is and the state set in the xleap Unit Editor's "Edit selected atoms" table is
The default state from which to start the perturbation is usually because the coordinates which are carried from EDIT to PARM to SANDER to GIBBS correspond to the PREP state. However, you can equilibrate at either (or any arbitrary value of
Set ISLDYN (line 14) to +-2 or +-3;
Set NRUN (line 5) to 1;
Set NSTLIM (line 8) to the number of steps of equilibration desired;
Set ALMDA (line 14) to the value of
at which equilibration is to take place;
And set NSTMEQ (line 14) to any value greater than NSTLIM.
The program is capable of handling periodic boundary conditions with the solute in a solvent bath either with constant volume or constant pressure. All the data required for boundary conditions is passed from the EDIT and PARM modules. Additionally, it is possible to decouple the free energy into electrostatic and van der Waals contributions, if desired.