Update toppar files and examples for constant-pH MD 67/5067/4
authorradakb <brian.radak@gmail.com>
Tue, 9 Apr 2019 19:01:43 +0000 (15:01 -0400)
committerJim Phillips <jim@ks.uiuc.edu>
Mon, 15 Apr 2019 21:06:17 +0000 (16:06 -0500)
commit117f7b6cca7e92dab49517b9e7d3cbf14b01ade6
tree45cc08c7d64d71860c166d3a70f0b80271ed59f5
parent99a50111a4236411599f4900f1798dbce91c74ec
Update toppar files and examples for constant-pH MD

-- NAMD specific force field files for constant-pH MD are now given
   in the lib/namdcph/toppar directory. This includes .prm, .rtf. and
   .json files that contain ONLY new parameters.

-- The (old syntax) examples have been updated and simplified.
   The acetic acid example has been pared down in the number of files
   and the omtky3 protein example has been replaced with the bbl
   protein example from the tutorial (this one is slightly simpler).

-- A limited number of force field files from the MacKerell group have
   been included so that these example can run "out of the box".
   These have been heavily disclaimed and print a warning to the user
   that the parameters are good for no other purpose but to make the
   examples run -- the MacKerell group agrees that this is an
   acceptable middle ground between flat out redistributing their
   parameters and a link to their website has been included in the
   message.

Change-Id: I9a706a40837087163e505fe4197367dfb4d02187
33 files changed:
lib/namdcph/examples/ace/ace.namd
lib/namdcph/examples/ace/ace_restart.namd
lib/namdcph/examples/ace/topology/ace.coor [deleted file]
lib/namdcph/examples/ace/topology/ace.pdb
lib/namdcph/examples/ace/topology/ace.psf
lib/namdcph/examples/ace/topology/ace.vel [deleted file]
lib/namdcph/examples/ace/topology/ace.xsc
lib/namdcph/examples/ace/toppar/conf_cph36_cgenff.json [deleted file]
lib/namdcph/examples/ace/toppar/par_all36_cgenff.prm [deleted file]
lib/namdcph/examples/ace/toppar/par_all36_solvent.prm [deleted file]
lib/namdcph/examples/ace/toppar/par_cph36_cgenff.prm [deleted file]
lib/namdcph/examples/ace/toppar/top_cph36_cgenff.rtf [deleted file]
lib/namdcph/examples/bbl/bbl.namd [new file with mode: 0644]
lib/namdcph/examples/bbl/topology/bbl.pdb [new file with mode: 0644]
lib/namdcph/examples/bbl/topology/bbl.psf [new file with mode: 0644]
lib/namdcph/examples/bbl/topology/bbl.xsc [moved from lib/namdcph/examples/omtky3/topology/omtky3.xsc with 51% similarity]
lib/namdcph/examples/omtky3/omtky3.namd [deleted file]
lib/namdcph/examples/omtky3/topology/omtky3.coor [deleted file]
lib/namdcph/examples/omtky3/topology/omtky3.hmr.psf [deleted file]
lib/namdcph/examples/omtky3/topology/omtky3.pdb [deleted file]
lib/namdcph/examples/omtky3/topology/omtky3.psf [deleted file]
lib/namdcph/examples/omtky3/topology/omtky3.vel [deleted file]
lib/namdcph/examples/omtky3/toppar/conf_cph36_prot.json [deleted file]
lib/namdcph/examples/omtky3/toppar/par_all36_solvent.prm [deleted file]
lib/namdcph/examples/omtky3/toppar/top_all36_prot.rtf [deleted file]
lib/namdcph/toppar/conf_cph36_cgenff.json [new file with mode: 0644]
lib/namdcph/toppar/conf_cph36_prot.json [new file with mode: 0644]
lib/namdcph/toppar/par_all36_prot.prm [moved from lib/namdcph/examples/omtky3/toppar/par_all36_prot.prm with 97% similarity]
lib/namdcph/toppar/par_cph36_cgenff.prm [new file with mode: 0644]
lib/namdcph/toppar/par_cph36_prot.prm [moved from lib/namdcph/examples/omtky3/toppar/par_cph36_prot.prm with 93% similarity]
lib/namdcph/toppar/top_cph36_cgenff.rtf [new file with mode: 0644]
lib/namdcph/toppar/top_cph36_prot.rtf [moved from lib/namdcph/examples/omtky3/toppar/top_cph36_prot.rtf with 94% similarity]
lib/namdcph/toppar/toppar_water_ions.str [new file with mode: 0644]