database:

(1) Physics finder

Computer Simulations :

(1)   NIC notes
(2)   collabrative computational project5 (ccp5)
(3)   D. Frenkel's notes
(4)   thesis_collection01
(5)   simulations - verlet list, cell list
(6)   simulation - review - thesis
(7)   P.J. Rossky's homepage
(8)   force field for polymers - caltech
(9)   thesis collection - caltech (Goddard's group)
(10) list of simulation softwares
(11) complete list of simulation softwares
(12) md related links
(13) md simulations of biomembrane
(14) caltech thesis collection
(15) Stillinger's publication list
(16) W.L. Jorgenson's homepage
(17) SH_Schiffer's notes on simulation
(18) MOPAC - manual
(19) David. J. Wales homepage - energy landscape
(20) molecular structure - database
(21) find crystal symmetries
(22) source forge - site map - software map
(23) list of simulation softwares
(24) chemistry softwares for linux
(25) list of simulation software
(26) Walker's group - experiment - liquid interfaces
(27) unit conversion
(28) all about computers
(29) good site for numerical recipes
(30) list of md softwares
(31) thesis collection - pennstate
(32) Institute of theoretical physics-UCSB-reviews,talks,etc...
(33) free science - books, softwares
(34) periodic table - complete
(35) findtutorials
(36) GNUplot - good tutorial
(37) List of simulation softwares - accelrys
(38) molecular animation
(39) CCL - mailing list
(40) CHARMM - documentation

 Force field development :

 (1) NASA's research centre
 (2) List  of  references for  force field parameters
 (3) accelrys notes on force fields
 (4) cerius2 force field notes

Classical Molecular dynamics codes :

(1)   code by Preston Moore (CM3D)
(2)   EGO
(3)   GROMACS
(4)   GROMOS (Van Gunsteren)
(5)   FANTOM (To find the low-energy conformations of polypeptides)
(6)   DL_POLY
(7)   DLPROTEIN
(8)   NAMD
(9)   PINY_MD
(10) FIST
(11) NEMD
(12) GAMESS
(13) moil (cornell university code)
(14) X-PLOR
(15) camposASE
(16) MDCASK - parallel
(17) MMTK - Molecular Modelling Tool Kit
(18) XMD (EAM,Stilinger-Weber,Tersoff MD)

Quantum simulations :

(1) NWchem
(2) Download codes from CCLRC
(3) PWscf - For electronic structure calculations
(4) SIESTA
(5) Abinit

 Car-Parrinello Molecular Dynamics :

 (1) Download codes from democritos
 (2) FPMD - For variable cell CPMD
 (3) CP - For variable cell CPMD (Car's group)
 (4) CPMD
 (5) CP2K
 
 
 Molecular Visualization programs :

 (1)   gOpenMol
 (2)   MDDisplay
 (3)   XCrySDen
 (4)   Molden
 (5)   VMD
 (6)   Xmovie
 (7)   opendx
 (8)   xmakemol
 (9)   gamgi
 (10) XMview/CMview
 (11)  jmol

 Plotting :

 (1) xmgr
 (2) xmgrace
 (3) gnuplot
 (4) PGplot
 (5) splot
 (6) mathplot
 (7) ptplot (berkeley)

  Graph theory :

  (1)  matrices for chemical bond

  Fortran 90 :

  (1) good tutorial
  (2) Intro to Fortran90

  Statistical mechanics

  (1)  "hunting spot" for stat. mech.

   math libraries for different platforms:

   IBM : essl libraries

   (1) essl - documentation-01
   (2) essl - documentation-02
   (3) math libraries

   MPI tutorials :

   (1) MPI - from llnl
   (2) MPI - MD
   (3) MPI - MD - sandia

  PYTHON Tutorials:

   (1) K_Hinsen's tutorial - useful for MD


  LINUX :

   (1) linux software encyclopedia
   (2) linux security - tutorial
   (3) Intel

  Numerical programs:

  (1) numerical_fullerton
  (2) Search for math packages - GAMS-NIST
  (3) numerical programs - Pozrikidis

  OpenGL  :

  (1) Mesa
  (2) f90gl
  (3) f90gl_portland