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3.3

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54 issues   (54 closed — 0 open)

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Bug #19: R-B dvdl is always nonzero
Bug #20: g_rms uses incorrect masses when reference is a PDB/GRO file
Bug #21: grompp treats comb-rule 3 as comb-rule 1 for LJ and LJ14
Bug #24: trjconv -split fails
Bug #25: g_hbonds+Gromacs version 3.3
Bug #26: bug in mdrun -rerun in gromacs 3.2.1 and 3.3; energies depend on box sizes and initial configuration in tpr file
Bug #27: QM/MM bugs
Bug #28: Extra semicolon in tools/config.h causes compilation failure with some compilers
Bug #29: gmx_fft_fftw3.c compilation error
Bug #31: lipid membrane simulation crashed using 3 fs time step with 3.3
Bug #32: bug in dihedral restraints code causes restraint force often to be in the wrong direction
Bug #33: Inconsistent sign convention for calculation of angles between g_angle and angle restraints
Bug #35: trjconv does not read velocities from g96 file.
Bug #36: two errors concerning trjconv -b -e
Bug #37: Implicit water constraints silently break conjugate gradient mimization
Bug #38: -dist option does not work in g_hbond version 3.3
Bug #39: Generation of initial velocities counts dummy atoms as normal atoms.
Bug #40: freeze groups on protein causes log file runaway during equilibration with constant pressure, even with weak coupling
Bug #41: How to change the Memory allocation function in Gromacs-3.3
Bug #43: turning on free energy turns off angle restraints
Bug #44: genbox or NS does not return allocated memory
Bug #45: pdb2gmx crashes when force field files in workdir
Bug #46: Constraint or not turned off on slaves
Bug #47: no manual for 3.3
Bug #48: Gromacs compilation error with lam/mpi
Bug #49: Wrong image convention for evaluating dummy atoms.
Bug #50: grompp -check14 SEGVs
Bug #51: the failure of double precision minimization
Bug #52: periodicity not handled correctly for dihedrals computed with g_angle
Bug #53: Angle definitions maybe wrong in g_chi
Bug #54: Compile fixes: enums aren't ints, and typename is now a reserved word
Bug #55: Internal XDR functions are broken on some big endian systems.
Bug #56: Pull code and Index group problem
Bug #57: g_hbond -g is broken
Bug #58: steepest descent minimization works with ns_type=simple but not ns_type=grid
Bug #59: Wrong LJ energies on Apple Mac OS X with Myrinet
Bug #61: dihedral restraint force constant not converted from degrees
Bug #62: g_hbond problem
Bug #63: eneconv produces NaN
Bug #64: pdb2gmx assigns non-existant atom (H211) when processing RNA
Bug #65: pdb2gmx(ver3.3) cannot link Fe(HEME) to NE2(HIS)
Bug #83: trjconv failing to read trajectory
Bug #96: intermediate restarts of simulations dont match
Bug #99: trjconv: broken molecules with -pbc whole; molecules out of box with -pbc com
Bug #100: interference between restraint definition and internal dihedral angles
Bug #104: periodicity not handled correctly in trjconv when converting to pdb
Bug #112: negative eigenvalues from g_covar
Bug #115: double frames after use of eneconv -f file1.edr file2.edr
Bug #123: Steepest Descents did not converge to Fmax < 1000 in 101 steps.Potential Energy = -4.1569785e+06Maximum force = 1.2874710e+04 on atom 19013Norm of force = 8.6780125e+04[unset]: aborting job:Fatal error in MPI_Send: Error message texts are no...
Bug #129: free_energy=yes affects energies at lambda=0
Bug #138: steepest descents exits with a segmentation fault; tweaking coordinates resolves
Bug #178: mdrun crashes with segmentation fault when using harmonic position restraints
Bug #180: g_sas with 3.3 and 3.3.2 gives different results
Bug #190: rerun interaction energy components error