solvate

This task simply performs a standard psfgen run that invokes the solvate and autoionize VMD plugins to make a system solvated by TIP3P water. It is typically specified using its name only. A prototypical usage example is below:

tasks:
  - fetch:
      sourceID: 6pti
  - psfgen:
  - md:
      ensemble: minimize
  - md:
      ensemble: NVT
  - solvate:
      salt_con: 0.15
  - md:
       ensemble: minimize
  - md:
      ensemble: NVT

After minimizing and thermalizing (300 K) a newly built system, pestifer will then solvate it and autoionize to achieve a salt concentration of 150 mM, and then it performs a second minimization and thermalization.