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2010-11-24	Berk Hess	fixed segv in grompp due to gmxcpp not checking for...	commit \| commitdiff \| tree
2010-11-09	Berk Hess	added -resnr option to editconf	commit \| commitdiff \| tree
2010-11-09	Berk Hess	fixed compiler warning in pdb2gmx.c	commit \| commitdiff \| tree
2010-11-05	Berk Hess	pdb2gmx now puts atoms with cgnr=-1 in separate charge...	commit \| commitdiff \| tree
2010-11-04	Berk Hess	Fixed md.log being opened twice when appending, which...	commit \| commitdiff \| tree
2010-11-02	Berk Hess	fixed incorrect print in fatal error on charge group...	commit \| commitdiff \| tree
2010-11-02	Berk Hess	proper defined of MAX_CHARGEGROUP_SIZE=32 in a single...	commit \| commitdiff \| tree
2010-10-28	Berk Hess	added HEM to HEME renaming for Gromos and Charmm ff's	commit \| commitdiff \| tree
2010-10-28	Berk Hess	fixed pdb2gmx chain merging bug (bugzilla 544)	commit \| commitdiff \| tree
2010-10-26	Berk Hess	fixed cycle print type cast issue on certain platforms...	commit \| commitdiff \| tree
2010-10-21	Berk Hess	clarified make_ndx error message	commit \| commitdiff \| tree
2010-10-19	Berk Hess	changed enxio warning into fatal errors by default...	commit \| commitdiff \| tree
2010-10-18	Berk Hess	fixed atom type name case for methanol.itp in gromos43a1.ff	commit \| commitdiff \| tree
2010-10-18	Berk Hess	fixed possible overflow of unused variable in lincs	commit \| commitdiff \| tree
2010-10-18	Berk Hess	added checks for rare events that would make variables...	commit \| commitdiff \| tree
2010-10-15	Berk Hess	more fixes for TPI with PME, now really fixed bugzilla 590	commit \| commitdiff \| tree
2010-10-13	Berk Hess	fixed g_velacc -m not automatically using -s	commit \| commitdiff \| tree
2010-10-12	Berk Hess	added note to g_density for using g_energy for normal...	commit \| commitdiff \| tree
2010-10-12	Berk Hess	fixed incorrect dispersion correction for TPI with...	commit \| commitdiff \| tree
2010-10-08	Berk Hess	fixed typo in checkpoint warning	commit \| commitdiff \| tree
2010-10-08	Berk Hess	made combination of tpi and pme work again in parallel	commit \| commitdiff \| tree
2010-10-08	Berk Hess	fixed combination of tpic with pme, pme mesh energy...	commit \| commitdiff \| tree
2010-10-05	Berk Hess	made grompp mdp input file non-optional, fixes bugzilla 577	commit \| commitdiff \| tree
2010-10-05	Berk Hess	added fail-safe check for OpenMM with double precision	commit \| commitdiff \| tree
2010-10-05	Berk Hess	renamed mdp setting Ace-approx to Ace-approximation	commit \| commitdiff \| tree
2010-10-05	Berk Hess	fixed completely incorrect pressure scaling with nstlist...	commit \| commitdiff \| tree
2010-09-30	Berk Hess	changed the grompp charge group radii to always check...	commit \| commitdiff \| tree
2010-09-25	Berk Hess	fixed case of opls atom types in share/top/ions.itp...	commit \| commitdiff \| tree
2010-09-22	Berk Hess	added a warning/note for bond oscillational periods...	commit \| commitdiff \| tree
2010-09-21	Berk Hess	added check for tau_t<=0 with integrator sd	commit \| commitdiff \| tree
2010-09-21	Berk Hess	fixed incorrect gmxcheck comparison of ir->separate_dhdl_file	commit \| commitdiff \| tree
2010-09-21	Berk Hess	improved the initial guess and fitting weights for...	commit \| commitdiff \| tree
2010-09-21	Berk Hess	removed g_analyze confusing fitting messages about...	commit \| commitdiff \| tree
2010-09-20	Berk Hess	fixed too small fixed array in grompp top reading ...	commit \| commitdiff \| tree
2010-09-17	Berk Hess	Revert "added GB non-polar solvation energy term to...	commit \| commitdiff \| tree
2010-09-17	Berk Hess	added GB non-polar solvation energy term to the log...	commit \| commitdiff \| tree
2010-09-17	Berk Hess	fixed free-energy giving a fatal-error when GB12, GB13...	commit \| commitdiff \| tree
2010-09-17	Berk Hess	added hint to g_traj warning	commit \| commitdiff \| tree
2010-09-16	Berk Hess	fixed the maximum print for g_traj -cv and -cf	commit \| commitdiff \| tree
2010-09-16	Berk Hess	fixed some minor issues with g_traj -cv and -cf	commit \| commitdiff \| tree
2010-09-16	Berk Hess	tau_t=-1 now works in grompp and with SD	commit \| commitdiff \| tree
2010-09-15	Berk Hess	fixed g_traj segv when ran without pbc	commit \| commitdiff \| tree
2010-09-15	Berk Hess	fixed charge group radius LJ check, which could produce...	commit \| commitdiff \| tree
2010-09-15	Berk Hess	added missing F_PIDIHS case to topsort free energy...	commit \| commitdiff \| tree
2010-09-15	Berk Hess	added GMX_MAX_THREADS env.var. to set the maximum number...	commit \| commitdiff \| tree
2010-09-14	Berk Hess	fixed memory allocation and access issues when reading...	commit \| commitdiff \| tree
2010-09-14	Berk Hess	grompp option -pp now always writes to cwd	commit \| commitdiff \| tree
2010-09-14	Berk Hess	g_density now normalizes every frame separately	commit \| commitdiff \| tree
2010-09-14	Berk Hess	g_density now normalizes with the average volume instead...	commit \| commitdiff \| tree
2010-09-14	Berk Hess	fixed incorrect reference position of position restraints...	commit \| commitdiff \| tree
2010-09-13	Berk Hess	fixed grompp -t frame choice for trajectories with...	commit \| commitdiff \| tree
2010-09-13	Berk Hess	state switches between the cpt and tpr file in mdrun...	commit \| commitdiff \| tree
2010-09-13	Berk Hess	added check and warning for no velocities in grompp...	commit \| commitdiff \| tree
2010-09-10	Berk Hess	turned on checkpointing with nstlist=0	commit \| commitdiff \| tree
2010-09-10	Berk Hess	removed the lower bound check on test particle insertion...	commit \| commitdiff \| tree
2010-09-10	Berk Hess	removed tip5p from charmm27.ff/watermodels.dat, since...	commit \| commitdiff \| tree
2010-09-10	Berk Hess	made sure the energy history from a checkpoint file...	commit \| commitdiff \| tree
2010-09-09	Berk Hess	added SSE overflow check for TPI	commit \| commitdiff \| tree
2010-09-09	Berk Hess	the force tables are now continued linearly from nearly...	commit \| commitdiff \| tree
2010-09-08	Berk Hess	improved the automatic choice of the number of PME...	commit \| commitdiff \| tree
2010-09-08	Berk Hess	added MCH3S atom type for Charmm for virtual sites...	commit \| commitdiff \| tree
2010-09-07	Berk Hess	changed the order of the outer loops in the fft5d transpose...	commit \| commitdiff \| tree
2010-09-07	Berk Hess	removed empty edr and xtc files with nm	commit \| commitdiff \| tree
2010-09-07	Berk Hess	removed (nan) average printing with normal modes	commit \| commitdiff \| tree
2010-09-07	Berk Hess	fixed crash with parallel nm with cut-off's	commit \| commitdiff \| tree
2010-08-31	Berk Hess	avoided creation of neighborlists without j-particles	commit \| commitdiff \| tree
2010-08-26	Berk Hess	fixed bug that caused corrupted checkpoint files	commit \| commitdiff \| tree
2010-08-26	Berk Hess	pdb2gmx now only allows a mismatch of a sign (iso any...	commit \| commitdiff \| tree
2010-08-24	Berk Hess	fixed pdb2gmx using start name iso end name for C-terminus	commit \| commitdiff \| tree
2010-08-24	Berk Hess	fixed bug in search_rtp introduced in previous commit	commit \| commitdiff \| tree
2010-08-24	Berk Hess	updated gmx_membed.c for a VV update	commit \| commitdiff \| tree
2010-08-24	Berk Hess	fixed pdb2gmx behavior for nearly matching residue...	commit \| commitdiff \| tree
2010-08-23	Berk Hess	removed the pdb2gmx -cwd option and updated the pdb2gmx...	commit \| commitdiff \| tree
2010-08-23	Berk Hess	pdb2gmx now prints the force field dir before the selection...	commit \| commitdiff \| tree
2010-08-23	Berk Hess	fixed mpi hang/crash with separate pme nodes and dd...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	added function do_cpte_n_reals to checkpoint.c	commit \| commitdiff \| tree
2010-08-20	Berk Hess	fixed automated DD/PME grid decomposition choice which...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	disabled optimized IBM BlueGene converts2ints macro...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	increased tpx_generation which should have been done...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	eneconv now copies the new delta_t entry	commit \| commitdiff \| tree
2010-08-20	Berk Hess	added dt to energy file frames	commit \| commitdiff \| tree
2010-08-20	Berk Hess	added free and some comment to deprecated close_trj	commit \| commitdiff \| tree
2010-08-20	Berk Hess	fixed segv's in g_anaeig	commit \| commitdiff \| tree
2010-08-18	Berk Hess	reduced the warning limit for Berendsen T-coupling...	commit \| commitdiff \| tree
2010-08-18	Berk Hess	removed the bNEMD boolean from the main MD loop and...	commit \| commitdiff \| tree
2010-08-18	Berk Hess	added some comment to group grompp assignment options	commit \| commitdiff \| tree
2010-08-18	Berk Hess	added group comparison to gmxcheck and print groups...	commit \| commitdiff \| tree
2010-08-18	Berk Hess	fixed possible pathe string buffer overflow in get_libdir	commit \| commitdiff \| tree
2010-08-17	Berk Hess	added function rescale_velocities	commit \| commitdiff \| tree
2010-08-16	Berk Hess	gmx_rmpbc now guesses ePBC again for each frame	commit \| commitdiff \| tree
2010-08-16	Berk Hess	gmx_rmpbc gets natoms passed again, without natoms...	commit \| commitdiff \| tree
2010-08-16	Berk Hess	put omp pragma's in fft5d.c between ifdef's	commit \| commitdiff \| tree
2010-08-16	Berk Hess	added openmp pragma's for the fft5d transpose routines	commit \| commitdiff \| tree
2010-08-16	Berk Hess	fixed mdrun writes tpidist.xvg on all nodes	commit \| commitdiff \| tree
2010-08-16	Berk Hess	fixed segv in mdrun with replica exchange	commit \| commitdiff \| tree
2010-08-16	Berk Hess	fixed fatal error in mdrun file appending with -multi...	commit \| commitdiff \| tree
2010-08-13	Berk Hess	gmxcheck now prints rmsd's as %g iso %f	commit \| commitdiff \| tree
2010-08-13	Berk Hess	moved full precision real format definition to simple.h	commit \| commitdiff \| tree
2010-08-12	Berk Hess	reverted the last, non-cosmetic change to pme.c	commit \| commitdiff \| tree
2010-08-12	Berk Hess	minor cosmetic changes in pme.c	commit \| commitdiff \| tree
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