source: parammd

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Diff Rev Age Author Log Message
(edit) @1625   3 years ehb Add pdb extends info to simplify box size determination
(edit) @1624   3 years ehb Fixed typo
(edit) @1061   5 years alexey paths
(edit) @1047   5 years alexey no plot results output if no requested
(edit) @1046   5 years alexey automatically identify and implement disulfide bonds for proteins..
(edit) @1045   5 years alexey Time is added to the movie plus minor issues…
(edit) @1044   5 years alexey Added energy plot. Plus corrected all logical scenarios. output …
(edit) @1043   5 years alexey Better visuzlized movie preparation process…
(edit) @1042   5 years alexey temperature plot added into analysis section…
(edit) @1041   5 years alexey Nicer movie representations (cratoons, vdw etc.)
(edit) @1040   5 years alexey Movies: camera veiw ritated..
(edit) @1038   5 years alexey unique names for videos with/no solvent solve the issue…
(edit) @1033   5 years alexey Movies with and without solvent..
(edit) @1030   5 years alexey Video of the MD trajectory is available (VMD, povray and ffmpeg are …
(edit) @1029   5 years alexey Ordering of messaging && adding actual MD simulations on top of …
(edit) @1028   5 years alexey error message box in case of smaller PBC than molecular size
(edit) @1027   5 years alexey Choice of salt added..
(edit) @934   5 years alexey upt
(edit) @933   5 years alexey output pdb correction
(edit) @932   5 years alexey able to generate solvated system with ions added
(edit) @930   5 years alexey user parameters
(edit) @928   5 years alexey Solvation/ion placing charmm modified scripts added..
(edit) @927   5 years alexey important upt on reading .pdb coord when columns merged (e.g. FG case)
(edit) @926   5 years alexey Determine size of the biomolecule, correct the size of the periodic …
(edit) @925   5 years alexey progress bar/text for NAMD minimisation
(edit) @924   5 years alexey updates related to NAMD minimization runs for both proteins and dna
(edit) @923   5 years alexey namd temp min upt
(edit) @905   5 years alexey charmm can be run for generation of multi-chain proteins..
(edit) @904   5 years alexey charmm template for proteins added (more work on multiple chaons yet..)
(edit) @902   5 years alexey cleaning up in the beginning
(edit) @901   5 years alexey HIS to HSD - added alias for processing proteins
(edit) @900   5 years alexey Parsing and preparation of multi-chain proteins .pdb files of various …
(edit) @899   5 years alexey updates on nucleic acids ppdb parsing - when chain's atoms/residues …
(edit) @889   5 years alexey i think i'm dome with parsing various DNA .pdb files..
(edit) @884   5 years alexey Covering more cases of various nucleic acid .pdb formats ... not ready yet
(edit) @883   5 years alexey generalization for read-in and charmm processing of arbitrary .pdb …
(edit) @879   5 years ehb Removed directives.json from svn (backed them up as alternate name) …
(edit) @833   5 years alexey charmm exe
(edit) @832   5 years alexey upt
(edit) @831   5 years alexey paramMD
(add) @830   5 years alexey paramMD - first sketch..
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