summaryrefslogtreecommitdiff
path: root/sim
AgeCommit message (Expand)AuthorFilesLines
2012-09-17tab crusading (python files)Bryan Bishop1-34/+34
2012-09-17whitespace crusadingBryan Bishop29-154/+154
2012-04-29remove bends_rcsid and bonds_rcsid from sim/src/newtables.cBryan Bishop1-2/+2
2010-12-16Applying contributed patches (see below)Thomas Fitzsimmons1-1/+1
2010-12-16Applying contributed patches for various makefilesThomas Fitzsimmons1-1/+6
2008-11-19Replaced "index" with "strchr".Mark Sims1-2/+2
2008-10-06C parser for AMBER force fieldEric Messick8-82/+359
2008-09-19make CQ pattern more specificEric Messick1-1/+3
2008-09-18allow NB, NC to match multiple Ns in same ringEric Messick3-5/+14
2008-09-18slight changes to Sulfur patternsEric Messick1-31/+12
2008-09-17AMBER atomtype patterns for S and miscEric Messick1-0/+92
2008-09-17AMBER atomtype patterns for HNOEric Messick4-0/+356
2008-09-15AMBER atomtype feedbackEric Messick10-78/+583
2008-08-06stricter interpretation of end line in .mmpEric Messick1-1/+4
2008-07-12Ignore clipboard items when simulatingEric Messick4-96/+122
2008-07-02Allow background minimization via GROMACSEric Messick2-18/+52
2008-07-01Allow background minimization via ND1Eric Messick3-1/+323
2008-05-30PAM3 with crossover does not explode in ND1 minimizeEric Messick2-20/+45
2008-05-30change bondpoints to hydrogens in regression testsEric Messick32-837/+988
2008-05-30add user parameters file to trace infoEric Messick3-5/+24
2008-05-29enable ND1 conversion of bondpoints to hydrogensEric Messick1-1/+3
2008-05-23add parameters for 3prime phosphateEric Messick2-3/+15
2008-05-20changes to non-bonded exclusionsEric Messick3-11/+91
2008-05-19Allow anchoring of PAM5 basepair virtual centersEric Messick4-16/+78
2008-05-16control neighbor searching from dialogEric Messick4-1/+11
2008-05-15partial implementation yukawa params in sim-params.txtEric Messick1-2/+2
2008-05-13specify PAM5 strut ends in table formatEric Messick4-15/+74
2008-05-12specify PAM5 strut ends in cartesian coordinatesEric Messick3-15/+86
2008-05-09/disabled/ code for GROMACS grid neighbor searchingEric Messick4-15/+129
2008-05-06Improve warning codeEric Messick1-1/+19
2008-05-05Add Yukawa potential to PAM3Eric Messick3-23/+83
2008-05-03Add Yukawa terms near crossoversEric Messick2-4/+114
2008-05-02pattern match feedback from ND1 to NE1Eric Messick4-111/+111
2008-04-16Yukawa potential between PhosphatesEric Messick3-94/+83
2008-04-14phosphate positioning, and latest PAM5 strutsEric Messick8-3/+160
2008-04-04ND1 now reads new lines in mmpformat 080328Eric Messick4-0/+127
2008-03-24change gromacs max iterations to 100000Eric Messick1-1/+1
2008-02-23added nstxout=10 to the .mdp fileBrian Helfrich1-0/+1
2008-02-01use preliminary strut model for gromacs PAM5Eric Messick2-3/+47
2008-01-24changes to python-pyrex simulator interfaceEric Messick10-726/+252
2008-01-17NE1 can pass sim-params.txt and gromacs vdw cutoffEric Messick6-23/+87
2008-01-16axial atoms with non-bonded forces and exclusionsEric Messick9-363/+504
2008-01-11The default install location of the Pyrex compiler on MacOS is /usr/local/bin .Russell D. Fish1-2/+12
2008-01-11Check that PAM5 always uses gromacsEric Messick1-4/+16
2008-01-10groove atoms in simulatorEric Messick8-293/+259
2008-01-07virtual sites for gromacs minimizeEric Messick11-404/+876
2007-12-21Adds missing strtok_r() implementation for Windows builds.Brian Helfrich1-0/+4
2007-12-18refactor process abort codeEric Messick4-6/+16
2007-12-11use bond dirs for PAM5 minimizeEric Messick8-194/+415
2007-12-11read pattern parameters from sim-params.txtEric Messick4-0/+45
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-05 04:34:56 +0000