
******************
**** Clusters ****
******************

This directory contains the solvent clusters. These can be in any plain or
packed format supported by VEGA. If you have speed problems, you can unpack
all data with WinDD.


Included clusters:
==================

* AMMONIA:
  58  ammonia cube in PDB FAT format (bzip2 packed). It was generated by VEGA
  starting from a monomer otimized with MOPAC. The obtained cluster was optimized
  with NAMD using CHARMM force field (30.000 steps). It contains 8.000 molecules
  (32.000 atoms).
 
* CH2CL2:
  50  dichloromethane cube in PDB FAT format (bzip2 packed). It was generated
  by VEGA starting from a monomer otimized with PCGAMESS. The obtained cluster
  was optimized with NAMD using CHARMM force field (30.000 steps). It contains
  1.000 molecules (5.000 atoms).

* CHCL3:
  50  chloroform cube in PDB FAT format (bzip2 packed). It was generated by
  VEGA starting from a monomer otimized with PCGAMESS. The obtained cluster
  was optimized with NAMD using CHARMM force field (30.000 steps). It contains
  1.000 molecules (5.000 atoms).
  
* POPC_CRYSTAL:
  ~60  lipid bilayer (palmitoyloleoylphosphatidylcholine, POPC) cube with
  solvatation waters in crystal phase. The starting structure is based on the
  Heller's model (see H. Heller, M. Schaefer, K. Schulten, "Molecular dynamics
  simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal
  phases", J. Phys. Chem. 97:8343-60, 1993).The cluster was optimized with NAMD
  using CHARMM force field and GASTEIGER charges (30.000 steps).
  
* POPC_CRYSTAL
  89x113x89 lipid bilayer (palmitoyloleoylphosphatidylcholine, POPC) with
  solvatation waterd in liquid phase. The file is in PDB FAT format (bzip2
  packed). The POPC monomer was optimized with MOPAC and the bilayer was built
  by VEGA. The two water layers are generated by VEGA also and assembled whit
  the POPC bilayer. The resulting cluster was optimized with NAMD using CHARMM
  force field (25.000 steps). It contains 256 POPC molecules and 17370 waters
  (69.262 atoms).
  

* FORMALDEHYDE:
  50  folmaldehyde cube in PDB FAT format (bzip2 packed). It was generated by
  VEGA starting from a monomer otimized with PCGAMESS. The obtained cluster was
  optimized with NAMD using CHARMM force field (30.000 steps). It contains
  2.197 molecules (8.788 atoms).

* METHANE:
  50  methane cube in PDB FAT format (bzip2 packed). It was generated by VEGA
  starting from a monomer otimized with PCGAMESS. The obtained cluster was
  optimized with NAMD using CHARMM force field (30.000 steps). It contains
  2.197 molecules (10.985 atoms).

* METHANOL:
  50  methanol cube in PDB FAT format (bzip2 packed). It was generated by
  VEGA starting from a monomer otimized with PCGAMESS. The obtained cluster
  was optimized with NAMD using CHARMM force field (30.000 steps). It contains
  2.744 molecules (16.464 atoms).
  
* OCTANOL-WATER:
  ~50  octanol-water cube in PDB FAT format (bzip2 packed). It was generated by
  VEGA starting from a single 4:1 octanol/water cluster optimized with Mopac.
  The obtained cluster was optimized with NAMD using CHARMM force field (30.000
  steps). A 750 ps (T = 300K) NAMD dynamics was performed and the best conformation
  was minimized (30.000 steps). It contains 748 molecules (16.644 atoms).

* WATER:
  50  water cube in PDB format (bzip2 packed). It was generated by Solvate
  1.0 software. It contains 3.928 molecules (11.784 atoms).

