CHARMM

Homepage: http://yuri.harvard.edu/
about hydrogen bond can be found at: http://www.scripps.edu/brooks/c29docs/hbonds.html

We distribute the source code of the CHARMM program with documentation to individual academic research groups for a $600 licensing fee. CHARMM runs on a variety of UNIX workstations, including the SG Indigo machines.

AMBER

Homepage: http://amber.scripps.edu/
about hydrogen bond: section 8.5 of the user manual.

Amber version 7 is distributed ONLY as a CDROM (of the source code, demos, and pdf manuals) accompanied with a printed manual.

Fees: Academic/non-profit/government: $400 (may be reduced or waived in special circumstances).

GROMOS

Homepage: http://www.igc.ethz.ch/gromos/
about hydrogen bond: see manual about PROAHB, PROMHB, PROCHB

This means that GROMOS96 is available for non-commercial institutes at the price of US $ 400,- which is meant to cover costs of administration (manual, correction letters, etc.) and distribution medium handling.

GROMACS

Hompage: http://www.gromacs.org/
about hydrogen bond: online manual
GPL software

Moldy

Homepage: http://www.earth.ox.ac.uk/~keithr/moldy.html
about hydrogen bond: no mention
GPL software

DL_POLY

Homepage: http://www.dl.ac.uk/TCS/Software/DL_POLY/
more info: http://www.cse.clrc.ac.uk/msi/software/DL_POLY/index.shtml
about hydrogen bond: http://www.cse.clrc.ac.uk/msi/software/DL_POLY/USRMAN2/node57.html

DL_POLY is supplied to individuals under a licence and is free of cost to academic scientists pursuing scientific research of a non-commercial nature. A group licence is also available for academic research groups. All recipients of the code must first agree to the terms of the licence.

NAMD

Homepage: http://www.ks.uiuc.edu/Research/namd/
about hydrogen bond: http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node116.html
probably post calculation

NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.

PMD

Homepage: http://tincan.bioc.columbia.edu/pmd/ (not working)
NAMD's predecessor (http://mycroft.ncsa.uiuc.edu/www-0/projects/)

MDynaMix

Homepage: http://www.fos.su.se/physical/sasha/md_prog.html


VMD
"VMD was developed by the Theoretical and Computational Biophysics Group 
 in the Beckman Institute for Advanced Science and Technology at the 
 University of Illinois at Urbana-Champaign."
http://www.ks.uiuc.edu/Research/vmd/allversions/cite.html
http://www.ks.uiuc.edu/Research/vmd/