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4.0

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94 issues   (94 closed — 0 open)

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Bug #243: free of inappropriate pointer in gmx_parallel_3dfft_destroy
Bug #244: mdrun memory error
Bug #245: Core dumped with grompp
Bug #246: Saving data with uneven step size in pullf.xvg file.
Bug #247: Parallel run, 4 CPUs crashes, 1 CPU works
Bug #248: grompp ignores double SOL lines in topololgy
Bug #249: Jump in pull force after ~ns of simulation
Bug #256: MD simulation crashes on 8 CPUs but not on 1 CPU
Bug #259: make_ndx crashes if *.tpr is used as input
Bug #260: Compile fails on hppa (PA-RISC) at gmx_cyclecounter.h:378
Bug #261: type 2 bonds with all-angle conversion makes grompp freeze
Bug #264: g_order not producing order parameters
Bug #267: distance restraints and domain decomposition error
Bug #268: energy minimization differs between CG with and without parallel
Bug #273: trjcat -demux fails with fio range checking error
Bug #278: make_ndx fails to create group corresponding to the last residue
Bug #281: Gromacs 4.0.2 and 4.0.3 unable to utilize multiple groups with settle
Bug #282: genbox -nmol 10 gives segmentation fault (version 4.0.3)
Bug #283: g_traj crashes with -mol option
Bug #284: couple-intramol not detected in .tpr files by gmxcheck or gmxdump
Bug #285: new mdp option "nstlist=-1" doesn't work with parallel runs
Bug #286: how to create a *.mdp file
Bug #287: SIGILL crash in nb_kernel with user tables and energygrp_table
Bug #288: out.gro problem
Bug #289: out.gro fail
Bug #290: uninitialized number of atoms in gro leads to confusing error message in grompp
Bug #291: outdated pull code text in gromacs 4 mdrun -h
Bug #292: pme problem in 4.0.3 results in memory allocation crash
Bug #293: pdb2gmx problem
Bug #295: editconf -f some.tpr -mead segfaults
Bug #296: Infinite loop in nb_kernel100_ia64_single subroutine
Bug #297: settle_type - gmx_fatal - constr.c
Bug #298: Segfault in a parallel particle decomposition run
Bug #304: sentences
Bug #305: trjconv -f traj.xtc -b X -e X -o out.gro yields an output frame when trj.xtc starts at a time greater than X
Bug #306: Discrepancies between 3.3.X and 4.0.X with energy/temperature drifts and premature termination of MD runs in 4.0.X
Bug #308: gmxcpp does not support #elif
Bug #313: gmxtest-4.0.4 fails for several kernel tests; likely due to LJ14 interaction calculations
Bug #315: append option continuing to write to previous trajectory crashed when dealing with a large traj.trr file
Bug #316: g_msd returns incorect value of self-diffusion coefficient for ngroup > 1
Bug #318: rerun produces inconsistent values for (shifted) virial when external force is used
Bug #320: Restart from Checkpoint with -nosum prints 0 initial temperature
Bug #321: cg / steep minimizations do not write modified configurations to trajectory
Bug #322: problem with particle decomposition in gromacs 4.0.4
Bug #324: 4.0.5's use of "restrict" keyword in altivec kernel breaks GCC compilers
Bug #327: g_mindist in 4.0.4 produces weird results
Bug #331: Minimization error "Can not invert matrix, determinant ="
Bug #332: Can not invert matrix, determinant =
Bug #333: SETTLE warning assumes MD, and reports a timestep under EM
Bug #334: g_hbond gives error when used with trajectory with positional restraint.
Bug #335: g_nmens does not write trajectories
Bug #337: generating pairs causing trouble when other nonbon_params are available
Bug #338: gro files incorrectly written
Bug #343: g_sas crash on x86_64
Bug #344: automake 1.11 + duplicates in pkginstall_HEADERS triggers install failure
Bug #345: gmxcpp incorrect path behavior
Bug #347: g_rmsdist results depend on the box
Bug #348: Hanging / Segfaulting Gromacs
Bug #350: Intermittent bug with pme_order == 6
Bug #353: Possible distance restraint bug in GMX 4.0.5
Bug #354: switching from Berendsen to V-rescale doesn't work if -nosum is used
Bug #356: g_sdf output has wrong normalization and wrong reference structure for more than one reference molecule
Bug #358: in g_rmsf, residue averaging with -res is broken
Bug #359: Missing bond in chloroform .rtp files
Bug #360: Grompp error due to incorrect reading of itp file
Bug #361: path buffer overflow in gromacs stable
Bug #362: MD problem when use "nstlist=-1" option with tabulated potential
Bug #364: NAN in g_anaeig -proj
Bug #370: install pkg-config file for better linking
Bug #372: install htmldoc in htmldir
Bug #375: constraints = hangles is broken
Bug #378: Gromacs 4 broken when compiled with Intel MKL
Bug #379: g_rdf hangs with -xy option and a provided topology file
Bug #382: g_mindist writing bogus information in atom-pairs file when -or is invoked
Bug #384: tabulated potentials derivative not interpolated correctly in some cases
Bug #388: Acetyl angle parameters missing from .rtp files
Bug #391: mdrun crashes in bcast_state when using particle decomposition
Bug #396: nan in g_anaeig entropy because of sqr instead of dsqr
Bug #397: g_wham error message wrong
Bug #398: Interpretation of MainChain is incorrect for ffamber
Bug #399: g_rdf -xy still hangs in version 4.0.7
Bug #402: g_dist and vsite
Bug #405: A strncmp call seems to be causing random occurences of buffer overflow
Bug #406: g_morph broken in Gromacs 4
Bug #433: replica exchange+constant pressure broken with one cpu per replica
Bug #455: Weird g_sorient failure
Bug #460: g_energy nmol switch
Bug #464: g_velacc in gromacs-4.0.7 seems to be producing some erroneous result.
Bug #481: Normal mode analysis produces wrong output in parallel
Bug #491: Constraints defined for a bond not working during simulation.
Bug #499: mdrun_mpi fails randomly
Bug #509: Last frame not written when re-starting from a checkpoint
Bug #519: g_energy displays wrong average
Bug #544: -chainsep