| Person |
Date |
Summary |
Description |
| Berk Hess |
17 Aug 2004 |
eneconv crash with starting time > 0 |
When the first file would start at a non-zero time eneconv would crash with a segmentation violation. This has been fixed. |
| Berk Hess |
17 Aug 2004 |
Dispersion correction and virial |
Fixed the virial correction which was incorrect in 3.2.0 and 3.2.1 (the pressure correction was correct). |
| Berk Hess |
17 Aug 2004 |
Dispersion correction and shifted potentials |
Implemented dispersion correction for shifted potentials. Improved the efficiency of the dispersion correction calculation. |
| Berk Hess |
17 Aug 2004 |
Free-energy with rcoulomb > rvdw |
Fixed a bug which would cause free-energy simulations to crash with a segmentation fault when rcoulomb > rvdw. |
| Berk Hess |
17 Aug 2004 |
Speed up with free-energy |
Free-energy runs now use much more solvent optimization. This gives a significant speed-up, especially with water. Also the neighbor-search with free-energy has been made more efficient. There is now almost no overhead for free-energy runs. |
| Berk Hess |
17 Aug 2004 |
Settle stability problem in single precision |
(AMBCONV) A precision problem has been fixed which could occur depending on the masses of the water atoms. With some combination of masses, for instance with the Amber forcefield produced with the AMBCONV script, the center of mass of each water molecule would shift every step by half a bit of a float. This would cause molecules to fly through the box. All forcefields supplied with Gromacs use the same water masses and have not been affected by this problem. |
| Berk Hess |
17 Aug 2004 |
Xmgrace displays g_anaeig output incorrectly |
Fixed incorrect scaling in xmgrace of the x-axis in files with multiple graphs produced by g_anaeig. |
| Berk Hess |
17 Aug 2004 |
eneconv bug when init_step > 0 |
When in any of the input files for eneconv the step number did not start at zero, which will happen when tpbconv is used in version 3.2, the averages in the output would be slightly off. This has been fixed. |
| Berk Hess |
17 Aug 2004 |
PME energy accuracy in single precision |
The PME and Ewald exclusion correction energy is now accumulated in a double precision variable. Previously the PME energy could have a relatively large error, 100 kJ/mol for a protein/water system, due to rounding problems. The forces and thus the sampling were correct. |
| Berk Hess |
17 Aug 2004 |
Reaction-field exclusion correction |
The reaction-field correction is now also applied to excluded atom pairs. The 1-4 energies are now reported without reaction-field correction. This mainly results in a shift in the Coulomb energy. There are minor changes in forces between excluded pairs that do not have 1-4 interactions. For a water box RF with a cut-off of 0.9 or 1.4 nm now gives a Coulomb energy within a few promille of PME. With old tpr files the old implementation will still be used, it can also be selected with reaction-field-old. |
| Berk Hess |
17 Aug 2004 |
Free-energy bug with soft-core |
Fixed a bug which was present in 3.2.0 and 3.2.1 which caused the normal LJ parameters to change after the first MD-step when soft-core potentials are used and 1-4 interactions are present. This will probably not have caused unnoticed errors as the LJ energies and dgdl changed significantly after this first step. |
| Berk Hess |
17 Aug 2004 |
Time in pull output |
Fixed the time in the pull output when init_t is not zero. |
| Berk Hess |
17 Aug 2004 |
Pull code and freeze groups |
The pull code is now aware of frozen atoms. Frozen atoms will no longer move during pulling. |
| David van der Spoel |
25 Aug 2004 |
rerun + dummies bug resolved |
Fixed a bug when doing a rerun with dummies. The graph would not be in sync with the coordinates since it only is created at neighborsearching time. Added an extra (conditional) mk_mshift call before constructing dummies. Added a further feature to the rerun option, that update (and shake) is only performed when velocities are present in the trajectory (i.e. never for xtc files) |
| Berk Hess |
27 Aug 2004 |
Removed mdp option bd-temp |
The mdp option bd-temp has been removed, its function is replaced by ref-t. Old run input files are converted correctly. |
| Berk Hess |
27 Aug 2004 |
New mdp option deform |
The non-equilibrium MD option deform has been introduced. It sets velocities for deformation of the (triclinic) box. It can be used to strain or shear a solid or a liquid. |
| Erik Lindahl |
29 Aug 2004 |
Added the Encad and Gromos45a3 force fields |
I've had Michel's Encad force fields working for several months, but finally decided to add it to the repository. This also involved added the Encad-style shift functions and water model (f3c) to be able to reproduce results exactly. While I was at it, I also added the version of Gromos45a3 that Alessandra contributed. |
| Erik Lindahl |
30 Aug 2004 |
Fixed bug with vectorized 1/sqrt with IBM MASS |
I've fixed two minor bugs that caused complete crashes: 1. When aligning memory it didn't work on 64-bit machines. I don't think we ever did it for any 64-bit machine, thouh. 2. There was a bug in the innerloop that caused it to crash hard when using the IBM MASS library for vectorized invsqrt. |
| David van der Spoel |
30 Aug 2004 |
eneconv without time 0 |
Patch for the case that the energy files did not start at time 0 Included in 3.2 patch branch and normal CVS |
| Berk Hess |
30 Aug 2004 |
Replica exchange |
Replica exchange has been implemented. It uses the -multi functionality of mdrun to run replicas in parallel. |
| Berk Hess |
31 Aug 2004 |
Fixed bug with ewald_geometry = 3dc |
Fixed bug where the ewald_geometry=3dc correction was only used when surface_epsilon was not zero, which is the default value, meaning ewald_geometry=3dc had no effect in most cases. |
| David van der Spoel |
6 Sep 2004 |
fixed bug in mpich-parallel runs |
Implemented a workaround for a bug in some parallel MPICH runs that never finished. The background for this was that the MPI_Finalize call did not return, and hence user jobs would not stop. |
| David van der Spoel |
6 Sep 2004 |
error messages |
The fatal_error function was replaced by a more flexible set of routines that give more informative error messages. |
| David van der Spoel |
7 Sep 2004 |
new feature in g_analyze |
Added option in g_analyze to compute an integral of e.g. a correlation function with error bars. |
| David van der Spoel |
7 Sep 2004 |
tip4p.itp updated |
Fixed an error which would compute intramolecular interaction in the case a flexible model was used. |
| David van der Spoel |
24 Sep 2004 |
MNO solvent bug |
A bug in the inner loop for special solvents where both the Coulomb and the LJ are shifted was fixed. The bug would lead to the LJ interaction being computed incorrectly, and would most often result in a crash with weird energies. |
| Erik Lindahl |
27 Sep 2004 |
MNO solvent bug in 3dnow assembly loops |
Fixed the previously mentioned bug in the 3DNow assembly loops too. |
| Erik Lindahl |
27 Sep 2004 |
Added GROMOS96 53a5 and 53a6 force fields |
The new versions of Gromos96 (contributed by Allesandra) have been added to the distribution, and the static choices in pdb2gmx. |
| David van der Spoel |
28 Sep 2004 |
special solvents bug |
A bug in the inner loop for special solvents where both the Coulomb and the LJ are shifted or switched was fixed. The bug would lead to the LJ interaction being computed incorrectly, and would most often result in a crash with weird energies. Coulomb with PME plus shifted/switched potential is also affected (but only for special solvents, like TIP4P water, and not for SPC(/E) or TIP3P). |
| Berk Hess |
29 Sep 2004 |
neighborlist optimization |
Optimal neighborlists are now generated. In previous versions pairs of 'i-atoms' without LJ and 'j-atoms' with LJ would still end up in innerloops which also calculated LJ interations. This optimization can provide a significant speedup for systems which contain many atoms with and without LJ, such as solvents (note that 3-site water models were already fully optimized). |
| Berk Hess |
4 Oct 2004 |
g_cluster bugfixes |
Fixed bug which caused incorrect avg rmsd for clusters and incorrect (rmsd for) middle structures. Changed name full linkage to single linkage (fixed several months ago). Fix error which almost always occured during the writing of the xpm output. Removed the -keepfree option. |
| Berk Hess |
15 Oct 2004 |
trjorder pdb B-factor output |
Fixed a bug which could cause trjorder to write nonsense distances in the B-factor field of pdb files. The ordering itself was correct. |
| Berk Hess |
18 Oct 2004 |
g_sas, area of a subgroup |
g_sas can now plot the solvent accessible of a subgroup of a molecule, for instance of one residue of a protein. |
| Berk Hess |
19 Oct 2004 |
g_energy RMSD and Fluct. |
Fixed g_energy RMSD and Fluct. output for energy files which do not start at step 0. Such energy files are produced when continuing runs with tpbconv. |
| Berk Hess |
21 Oct 2004 |
grompp, pairtypes with gen-pairs=yes |
Fixed problems which caused grompp to produce warnings and a fatal error when pairtypes where used in combination with gen-pairs=yes. |
| David |
24 Oct 2004 |
pmetest |
Developed a new program src/contrib/pmetest that reads a tpr file and a trajectory file and computes the longe range Coulomb interactions using the PME algorithm. Works in parallel as well. |
| Berk Hess |
27 Oct 2004 |
trjconv with -pbc nojump and fitting |
Fixed the problem in trjconv which caused the combination of -pbc nojump and fitting to produce 'jumped' results. |
| Berk Hess |
9 Nov 2004 |
pull code umbrella sampling |
Fixed problems in the pull code with umbrella sampling with multiple groups or an absolute reference. |
| Berk Hess |
15 Nov 2004 |
20 pull groups |
The pull parameter file now has an extra entry "ngroups". The maximum number of pull groups has been increased from 4 to 20. |
| David |
15 Nov 2004 |
segv with mdrun -h |
Fixed a SEGV in mdrun when called with the -h flag |
| Berk Hess |
8 Dec 2004 |
changed grompp warnings to errors |
All warnings issued by grompp about incorrect topology input have been converted to errors. |
| Berk Hess |
14 Dec 2004 |
Renamed dummies to virtual sites |
To avoid confusion with dummy masses, the notion dummy atom in Gromacs has been renamed to virtual (interaction-)site. The topology directives "dummies?" have been renamed to "virtual_sites?". Particle type "D" has been renamed to "V". Old topology files can still be read. |
| Berk Hess |
17 Dec 2004 |
FENE and quatic angle potentials |
Implemented the FENE (finite extensible nonlinear elastic) bond potential. Implemented a fourth order polynomial angle potential. |
| Erik Lindahl |
27 Dec 2004 |
Fixed block creation bug |
When creating blocks with stupid_fill, the last group was left out. This has lead to the genbox neighborsearching neglecting the last group in the system. |
| Erik Lindahl |
27 Dec 2004 |
Added TIP4P loop optimization |
The nonbonded kernels and neighborsearching has been updated to allow TIP4p-specific optimization as well as SPC. All references to the MNO general solvent loops have been removed. |
| Erik Lindahl |
27 Dec 2004 |
TIP4p assembly loops |
Assembly loops optimized for TIP4p have been added both for SSE & SSE2. There are also new assembly loops for standard coulomb or reaction-field combined with tabulated LJ, so now _all_ interactions except for buckingham are accelerated. |
| Erik Lindahl |
27 Dec 2004 |
X86-64 assembly loops |
SSE (single) and SSE2 (double) assembly loops have been added for the x86-64 architecture. These loops _should_ work on both Opteron/Athlon64 and Intel EMT64, but this far they have only been tested on AMD systems. Erik |
| Erik Lindahl |
27 Dec 2004 |
ia64 assembly loops |
Nonbonded kernels in both single and double precision ia64 assembly have been added. The kernels use software pipelining scheduled for the instruction latencies on Itanium2. The performance will likely be _very_ bad on Itanium1, but since that generation is pretty uncommon now they are enabled by default on ia64. If instruction latencies change in future generations, the innermost loops might have to be rescheduled. |
| Erik Lindahl |
27 Dec 2004 |
Multithreading for nonbonded kernels |
All assembly kernels now use compare-exchange instructions for multithreading. We still don't use multiple threads by default (need to fix neighborsearching), but this means they might require a slightly newer version of the gas assembler - one that supports "lock cmpxchg" to lock the bus in SMP systems. |
| Erik Lindahl |
27 Dec 2004 |
New solvent detection |
The solvent detection code has been rewritten from scratch: It now finds all charge groups that fulfill the conditions for either the SPC/TIP3p nonbonded kernels, or the TIP4P kernels. Parameters are compared between groups, and only the most abundant type is set to the optimized solvent. (The previous code never checked if the parameters matched between groups). |
| Erik Lindahl |
27 Dec 2004 |
Test systems for nonbonded kernels |
A new test_kernels directory has been added to the "test" module in cvs. This is not run by default, but inside the directory there are two perl scripts which will run all the systems and compare the results with those of Gromacs 3.2/3.3. Note that not all kernels will be available on all architectures; on e.g. ia64 the water loops are disabled when using assembly. |
| Erik Lindahl |
27 Dec 2004 |
Reverted atom order in TIP4p |
The TIP4p coordinates and itp files now have the atoms in standard order: OW HW1 HW2 MW Note that this is the only order which will enable the new TIP4p-specific assembly loops. |
| Berk Hess |
5 Jan 2005 |
pull code constraint distance |
Added an option to the pull code parameter file to set the constraint distance, instead of taking the distance from the input coordinates (which can still be done). |
| Berk Hess |
12 Jan 2005 |
g_analyze block averaging |
Improved the fit of the block averaging by fitting the sqaure, and improving the weights and the initial guess. Invalid fits should not occur anymore. |
| Berk Hess |
12 Jan 2005 |
Ewald and PME with epsilon_r not 1 |
Ewald and PME now also work correctly with dielectric constant epsilon_r not equal to 1. |
| David van der Spoel |
23 Jan 2005 |
support for dihedral principal component analysis |
Added support for dihedral PCA to g_angle. |
| Erik Lindahl |
2 Feb 2005 |
Fixed nonbonded parameter bug |
Hi, The code committed by Berk 2-3 weeks ago to enable sigma/epsilon values for individual nonbonded parameters caused a bug for force fields that uses scaling for 1,4 parameters. Previously, the parameters were first converted to c6/c12 and then everything was scaled. In the new version the are kept longer as sigma/epsilon, but this resulted in both the sigma and epsilon values being scaled. I've fixed it by checking for the combination rule, and only scale epsilon values when sigma/epsilon parameters are read. |
| Erik Lindahl |
2 Feb 2005 |
LAPACK, BLAS, and ARPACK stuff |
I've added a subset of the LAPACK and BLAS libraries to gmxlib, written in portable C. The user can optionally override it and use vendor-provided BLAS/LAPACK libraries instead. The ql77 diagonalizer code from EISPACK has been replaced with much faster LAPACK versions throughout the code. I've also added a small number of routines from ARPACK to support Arnoldi iterations for general eigenvalue problems. |
| Erik Lindahl |
2 Feb 2005 |
Sparse matrix representation for normal modes |
I've implemented sparse matrix representation both for the Hessian calculation and the actual diagonalization. The sparse representation can be used whenever cut-offs are used (instead of e.g. PME), and makes it possible to determine an arbitrary number of low eigenvectors for very large systems - the memory requirements are linear in system size! To support this I have changed the mtx format to be either full or sparse. The selection of full/sparse format is completely automatic and does not require any user intervention. |
| Erik Lindahl |
3 Feb 2005 |
Eigenvector format & eigenfrequencies |
The eigenvalues are now stored in the eigenvector files, so you don't have to provide the eigenval.xvg file separately. g_nmeig now also writes a separate file with eigenfrequencies correctly scaled to cm-1. |
| David van der Spoel |
8 Feb 2005 |
PME-User support |
Added support for a combination of PME and User determined coulomb potentials. The user has to take care that the combination of Coulomb and standard PME makes sense. |
| Berk Hess |
8 Feb 2005 |
tip5p atom order |
The tip5p atom order has been changed to the 'normal' order. Because of more optimization in the neighbor search the normal Gromacs innerloops now run tip5p much faster than the MNO solvent optimized loops. |
| Berk Hess |
21 Feb 2005 |
g_densmap |
Added the tool g_densmap which calculates 2D number-density maps. The map can be planar or axial-radial. Also xpm2ps has been adapted to correctly plot ticks for spatial instead of time or matrix element axes. |
| Berk Hess |
1 Mar 2005 |
test particle insertion |
Test particle insertion has been implemented. It is very efficient as it only calculates the interaction energy (no forces) of the test particle with the rest of the system. |
| Berk Hess |
1 Mar 2005 |
reaction-field NEC |
Renamed reaction-field-old (the reaction-field implementation of Gromacs version 3.2 and older) to reaction-field-nec: no exclusion correction, which gives a more useful description. |
| Berk Hess |
2 Mar 2005 |
Pull code AFM and umbrella fixes |
The contribution of the AFM and umbrella forces to the virial are now taken into account. The reaction forces on the reference group for AFM and umbrella pulling have now been added. |
| Berk Hess |
2 Mar 2005 |
Pull code AFM and umbrella fixes |
The contribution of the AFM and umbrella forces to the virial are now taken into account. The reaction forces on the reference group for AFM and umbrella pulling have now been added. |
| Berk Hess |
7 Mar 2005 |
pbc=full now works with constraints |
Simulations with pbc=full (for periodic molecules) can now be performed properly with constraints. Only LINCS is supported, not SHAKE. |
| Berk Hess |
11 Mar 2005 |
Pull code constraint virial |
With constraint pulling the constraint virial (and thus the total virial) is now also correct when the constraints between two pull groups passes over a box boundary. |
| Berk Hess |
11 Mar 2005 |
Virtual sites and virial |
Fixed (relatively) small jumps in the virial which could occur when the virtual site and/or atoms involved in the construction of the virtual site lie over a box boundary. |
| David van der Spoel |
11 Mar 2005 |
XTC - random access |
Added support for random access to xtc files, allowing for e.g. fast forward. Implemented by Filipe Maia. |
| David |
1 Apr 2005 |
changed format of hdb and tdb files |
The format of hydrogen database and termini database files has been changed in order to allow for user-specified names on generated hydrogens. |
| David |
2 Apr 2005 |
fixed bug in g_msd |
A bug was fixed that gave a SEGV when the -mol option was used in combination with the -trestart option when trestart was < trajectory length, i.e. when there were actual restarts. |
| David |
3 Apr 2005 |
new features in g_hbond |
Added functionality to compute hydrogen bond lifetimes and fixed SEGV bug in the hbmap option. |
| Berk Hess |
7 Apr 2005 |
Temperature coupling |
The Berendsen and Nose-Hoover temperature coupling now use the temperature at the half step. Nose-Hoover now uses a reversible integrator: Holian et al. Phys Rev E 52(3) : 2338, 1995 |
| Berk Hess |
7 Apr 2005 |
Kinetic energy |
The kinetic energy in Gromacs is now determined as the average of the kinetic energy of the velocities at the half steps around the full step. This is four times more accurate than the old method which used the full step particle velocities which were obtained as the averages of the half steps. |
| Berk Hess |
12 Apr 2005 |
trjconv -center |
Changed the -center option of trjconv to an enum which has the values no, tric, rect and zero so the user can define where the box should be centered. |
| Berk Hess |
12 Apr 2005 |
distances and pbc in tools |
The pbc_dx distance function which is used in many analysis tools now corrects for mutiple box-vector shifts and thus always produces correct distances. For normal mdrun output there was never a problem. But problems could occur with manipulated trajectories or output from other software packages. |
| Berk Hess |
20 Apr 2005 |
skipping frames in double precision |
When using a double precision compilation frame skipping with a single precision trajectory is now performed with a single precision margin instead of double precision. |
| Berk Hess |
21 Apr 2005 |
dispersion correction in large systems |
Fixed bug in the dispersion correction for systems with more than 46340 atoms. Reduced time for the average C6 calculation for dispersion correction in large systems from minutes to seconds. |
| Berk Hess |
22 Apr 2005 |
g_hbond reduced memory usage |
g_hbond used to always allocate an amount of memory proportional to the total number of donors times the total number of acceptors. This made analysis of more than a few thousand water molecules impossible. For half of the output options this memory allocation has been removed. |
| David van der Spoel |
7 May 2005 |
OPLS parameters |
Modified incorrect SIGMA values in ffoplsaanb.itp for united atom types. These types are not generally used and hence old simulations are correct. |
| Berk Hess |
19 May 2005 |
implemented mulitple user tables |
Seperate user tables can now be used for selected pairs of energy groups. This is set in the mdp file with the option energygrp_table. |
| Berk Hess |
19 May 2005 |
PME-User |
With coulombtype=PME-User mdrun now subtracts the PME mesh contribution from the user tables. |
| Berk Hess |
24 May 2005 |
corrected averages and fluctuations in md.log |
Since version 3.2 incorrect averages and fluctuations would be reported at the end of the md.log for simulations which were continued with tpbconv. This has been corrected. |
| Berk Hess |
1 Jun 2005 |
minimization with constraints |
During constraining in energy minimization atoms were moved inversly proportional to their mass. This has been fixed. Steepest descents with constraints now converges properly. |
| David van der Spoel |
2 Jun 2005 |
Added new filetype .pqr |
Input files for the MEAD electrostatics program can now be produced directly by editconf from a tpr file. |
| Berk Hess |
6 Jun 2005 |
generalized reaction-field |
Fixed an error in the generalized reaction-field. There was an incorrect factor 2 in the (kappa r_c)^2 terms in both the code and the manual. (The normal reaction-field was not affected) |
| Berk Hess |
6 Jun 2005 |
epsilon_rf |
Introduced a seperate mdp parameter for the relative dielectric constant of the reaction field: epsilon_rf. This avoids confusion and allows the use of a different epsilon_r and epsilon_rf for reaction field. Old mdp and run input files are still read correctly. |
| David van der Spoel |
9 Jun 2005 |
New option -[no]xvgr to analysis tools |
Added a new option to analysis tools to prevent the output of xvgr specific info like legends, title, axis title etc. |
| David |
11 Jun 2005 |
ndx file support in gmxcheck |
Added feature to analyze the content of an index file in the gmxcheck program. |
| Berk Hess |
17 Jun 2005 |
special pair interaction functions |
Up to now when shift, switch or user functions were used for the nonbonded interactions, these functions were also used for the pair interactions. Now with shift and switch the normal cut-off interactions are used for the pairs. For user functions a second table file is now read by mdrun when pair interactions are present. Berk |
| David |
5 Aug 2005 |
Constant pressure REMD |
Added support for constant pressure replica exchange MD. Can be turned off using a command line argument for backwards compatibility. |
| Berk Hess |
29 Aug 2005 |
finalization with mdrun -multi |
mdrun -multi (and replica exchange runs) would not call MPI_Finalize before finishing. In some cases this would lead to truncated or missing output files. This has been fixed. |
| Berk Hess |
30 Aug 2005 |
soft-core lambda power |
Implemented lambda power of 1 (now default) for the soft-core interactions in addition to the old lambda power of 2. |
| Erik Lindahl |
30 Aug 2005 |
Fixed table bug for switch/shift interactions |
The bCoulomb[] field was initialized incorrectly in the CVS version, which lead to coulomb cutoffs being assigned to LJ and vice versa for switch/shift interactions. This does not affect 3.2.1. |
| Erik Lindahl |
30 Aug 2005 |
Fixed logfile runaway |
mdrun now stops with an error message after 10,000 LINCS warnings. |
| Berk Hess |
30 Aug 2005 |
PBC problem with special topologies |
A PBC problem that has been in the code for many years has been fixed. This would only occur for special topologies, where not all atoms in a molecule are be connected by bonds, but they would still interact via other interactions, for instance distance restraints. The problem could also occur when running on multiple cpu's without constraints, which could cause molecules to be split over cpu's. |
| Erik Lindahl |
31 Aug 2005 |
Fixed LJ bug in x86-64 loops |
A rare bug in the LJ parameter assignment caused small potential errors in the updated x86-64 loops introduced last week. |
| Erik Lindahl |
31 Aug 2005 |
EM64t assembly loops |
The x86-64 loops have been ported to compile and work on em64t (Intel 64-bit extensions) architectures. |
| Erik Lindahl |
31 Aug 2005 |
Fixed segfault on ia32 SSE2 |
Fixed a stack error that caused segmentation faults on some double precision ia32 nonbonded loops. |
| David |
2 Sep 2005 |
Fixed cool quotes |
Cool quotes can now be turned off by setting an environment variable GMX_NO_QUOTES or by removing the gurgle.dat and/or bromacs.dat files. |
| David |
5 Sep 2005 |
Header in xvg files |
The header in xvg files now prints the command line used to generate the output file. |
| David |
24 Sep 2005 |
Moved system splitting code to mdrun |
The code that splits a simulation system into bits for a parallel calculation has been moved from grompp to mdrun. One does not need special multiprocessor topologies anymore. Shuffling has not yet been added. [4.0 only] |
| David van der Spoel |
4 Oct 2005 |
g_hbond bug fixes and new options |
Fixed horrible bug in g_hbond which would completely mess up the hbmap option. Added new feature to compute number of HB per hydrogen for comparison with Raman spectroscopy. In 3.3rc and 4.0. |
| Erik Lindahl |
5 Oct 2005 |
Builting parallel FFTs |
Added code to perform our own parallel FFTs using single-CPU 1d and 2d transforms. |
| Erik Lindahl |
5 Oct 2005 |
More FFT libraries |
Since we now have our own parallel FFTs we are no longer dependent on FFTW-2.1.x. The release-3-3-patches branch now contains wrappers for fftw2, fftw3, Intel MKL, and a builtin (slower) version of FFTPACK. Use the configuration switch --with-fft=XXX to select which implementation to use. /Erik |
| Berk Hess |
5 Oct 2005 |
fixed error in dihedral angle free-energy |
contribution In free energy simulations with perturbed proper and improper dihedrals a degrees to radians conversion factor had been missing in the contribution to dV/dlambda of the change in equilibrium angle. Note that the force and potential were correct, as well as the contribution of the change in force constant. |
| Erik Lindahl |
9 Oct 2005 |
Modified default cpp path |
The default preprocessor is now /usr/bin/cpp , which seems to be more common on modern systems. |
| Erik Lindahl |
11 Oct 2005 |
Using gromacs subdirectories in share & include |
We now use the standard pkgdatadir and pkgincludedirs by default, which means actual files are installed in share/gromacs/... include/gromacs/... even if the top-level prefix contains gromacs (e.g. /usr/local/gromacs). Previously the configure script contained an ugly hack where the subdirectory was added if the prefix did not contain gromacs or gmx, but this doesn't work with modern versions of rpmbuild. (It is also better to standardize on the same solution as the rest of the world rather than risk overwriting stuff in /usr/include...) |
| Erik Lindahl |
12 Oct 2005 |
Fixed incorrect dvdl term from R-B dihedrals |
Fixed reading of bonded types with explicitly specified parameters, so that B-state parameters are automatically set from the A-state if the are not given. This applies e.g. to the OPLS torsions that were specified with #defines, and gave rise to incorrect contributions to dvdl. |
| Berk Hess |
21 Oct 2005 |
frame counters |
The frame counters for reading trajectory and energy files now progessively print each, each 10th, each 100th and every 1000th frame. |
| Berk Hess |
25 Oct 2005 |
trjcat dt problems |
Fixed a problem in trjcat which could cause missing frames in the output when the timestep for the different input trajectories were not identical. |
| Berk Hess |
26 Oct 2005 |
gmxcheck -ab |
Added -ab option to gmxcheck which compare the A and B state topology from one run input file for free energy simulations. |
| Berk Hess |
3 Nov 2005 |
g_rdf normalization |
g_rdf did not take self exclusions into account for the normaliztion of rdf's when the reference and analysis group overlapped. For an rdf of a group of N particles with itself the rdf needs to be scaled up by N/(N-1). This correction has been added now. |
| Berk Hess |
10 Nov 2005 |
grompp default bonded parameters for perturbed atoms |
For free-energy sytems where atomtypes are different in the A and B state and default parameters for bonded interactions were searched for both the A and B state and could be found for the A state, but could not be found for the B-state, the parameters for both the A and B state would silently be set to zero. Now the A-state parameters are copied to be B-state and a warning is issued. |
| Berk Hess |
6 Dec 2005 |
SD and pull code constraints |
Fixed the combination of SD and pull code constraints. The velocities and pull forces would be far too large (could not have caused silent errors). |
| Berk Hess |
15 Dec 2005 |
trjconv -split file names |
Fixed a bug which caused trjconv -split to produce filename like: (null)_0_(null) |
| Berk Hess |
15 Dec 2005 |
Frame selection problems with -tu |
Fixed rounding problems with the time unit option for analysis tools -tu was set to something different than the default ps. This problem could cause frame to be skipped or selected incorrectly. |
| David van der Spoel |
29 Dec 2005 |
g_energy selection |
The selection mechanism in g_energy was changed to accept strings rather than numbers. |
| David van der Spoel |
2 Feb 2006 |
removed disco and friends |
The disco and cdist programs, an implementation in GROMACS of the CONCOORD program suite by Bert de Groot have been removed. Users are advised to use CONCOORD instead. [3.3 and 4.0] |
| Berk Hess |
3 Feb 2006 |
pair types for free-energy decoupling |
Added new pair type 2, which is identical to the standard type 1, except that it only the A-state charges and LJ parameters. Added new pair type 3, which use the non-scaled charges and the normal non-bonded parameters, also only from the A-state. |
