Additions and Bug Fixes

29 Dec 2023

• Fixed bug in constraint satisfier that was causing it to freeze up at the beginning of a simulation

19 Oct 2023

• Fixed bug in born_integral that was making it crash when using the -atoms option.

6 Oct 2023

• Added dummy molecule feature to help in defining reaction criteria
• Put in a better algorithm for initially satisfying constraints

14 Jun 2023

• Fixed a bug in born_integral that could cause it to crash with noncubic grids

27 Apr 2023

• added an option "-atoms" to "born_integral" to compute the sum over atoms rather than grid points, as SDA does

25 Jan 2023

• Fixed bug that was causing weighted-ensemble simulations to crash

23 Jan 2023

• Fixed recently-introduced bugs that caused freeze-ups for the case of no constraints or constant time steps.

7 Dec 2022

• Added hydrophobic interactions
• Improved constraint algorithm
• bug fix in pathway code
• bug fix for case of flexible chain attached to core
• changed polar desolvation force to match expression in SDA software
• Desolvation grids now exactly mirror electrostatic grids; used to be just inner grid
• Added polar desolvation force for chains
• Possible to specify Lennard-Jones parameters using epsilon and sigma
• added some defaults to process_trajectory

13 Jun 2022

• Fixed a bug that was causing weighted-ensemble bin-building to crash

2 Jun 2022

• An "undocumented feature" was the fact that Browndye required the excluded and one-four atoms in the chain file to have smaller indices than the listing atom. This has been corrected; excluded and one-four atoms can be listed in any order.

30 May 2022

• Updated vtf_trajectory to accept its input through standard input rather than with the traj flag.

18 May 2022

• Fixed a bug in bd_top : it was not propagating the constant_dt from the input file to the simulation file.

7 Mar 2022

• Fixed a bug which was causing errors in cases of chains attached to cores.
• Fixed a bug in propagation of core orientations; could have modest effects on association rates.

12 Feb 2022

• Rewrote the hydrodynamic interactions to eliminate a numerical instability.
• Fixed a bug which was causing an error in the timescale of chain simulations (but not cores) with hydrodynamic interactions. No effect on equilibrium properties or probabilities, but the timescale was low by a factor of 6 π.

28 Jan 2022

• Added the no_nam to prevent bimolecular rate constant calculation for case of two groups with a reaction.

25 Jan 2022

• Added the ability to restrain the distance between two given atoms to be below a given value.
• Because of the new restraint feature, the number of groups is no longer limited to 1 or 2.
• Fixed bug that was causing troubles in constraint initialization for the case of more than one chain.
• Fixed errors in the COFFDROP files coffdrop.xml and connectivity.xml that affected the model for phenylalanine.

12 Jan 2022

• Fixed some bugs that were keeping the chain freezing and unfreezing from working properly
• Updated bd_top to allow more chain information to be propagated to the simulation file.
• Fixed a bug in computing rotational diffusivity for the rigid cores. This affected only the case of no hydrodynamic interactions; could slightly affect rate constants.

3 Jan 2022

• Including a new constant_dt option for each chain. If any chains are unfrozen and have a time step value for this tag, the simulation will proceed with the smallest constant_dt value. The documentation is updated.
• Fixed an error in the documentation regarding the chain file. For example, the bond tags are all to be enclosed inside the bonds tag, and likewise for other structures.
• Included a check on the XML input from the chain file
• Added a new program chain_atom_distances . It can be used to output atom-atom distances from a trajectory of a simulation of a single chain.

14 Dec 2021

• Fixed a bug that was causing simulations with constraints and constant time steps to crash occasionally.

3 Dec 2021

• Added option to use a constant timestep; this is used by including the tag < constant_dt > under < time_step_tolerances >. This will be useful for the COFFDROP model, where a constant timestep of 0.05 ps is recommended.
• Added option to compute_rates_we to convert the results file from we_simulation to the format output by nam_simulation . This is used by including the flag -nam on the command line.

18 Nov 2021

• Fixed problem that was causing chains with occasional updates to the hydrodynamics to crash
• Put an additional constraint satisfier at the start for cases where the inputs don't have their constraints satisfied
• Added missing bonds for the terminal N and O pseudoatoms in the COFFDROP model
• Changed dt in trajectory file to be elapsed time between outputs rather than Brownian time step at that point

4 Oct 2021

• Changed output_trajectory to output time steps instead of absolute time.
• Fixed the resulting inconsistency in vtf_trajectory .

28 Sep 2021

• Fixed a bug that was sometimes causing the b-radii to be larger than necessary

2 Sep 2021

• Fixed and improved the weighted-ensemble method
• Ammended the manual to include the programs make_rxn_pairs and make_rxn_files.

10 Aug 2021

• Fixed process_trajectories so it will output the last state in the trajectory.

28 Jul 2021

• Fixed newly introduced bug in advancing rigid core time steps

21 Jul 2021

• Fixed problem with empty chains (used for connecting core atoms directly with springs)

15 Jul 2021

• Improved time step selection near reaction

7 Jul 2021

• Fixed some bugs that were preventing a successful core-with-loop simulation

2 Jul 2021

• Fixed bug that made bd_top crash

1 Jul 2021

• Fixed a bug with assigning custom Lennard-Jones parameters to specific atom pairs

29 Jun 2021

• Fixed a bug in trajectory outputter that was affecting more than one core in a group
• Made the Lennard-Jones parameters A and B consistent with the documentaion, and corrected the documentation

25 Jun 2021

• Cleaned up logic of freezing chains and cores
• Several bug fixes

8 Apr 2021

• Fixed a bug that was causing incorrect rotational updating for the rigid cores
• Implemented the latest constraint algorithm

20 Feb 2021

• Fixed a bug that was causing incorrect rotational mobility for two rigid cores for the case of no hydrodynamic interactions

9 Feb 2021

• Added alerts to unused XML tags in input to bd_top
• Fixed bug in automatic calculation of b-radius

8 Feb 2021

• Fixed unwanted output to standard output, left in from a debugging run
• Fixed spurious warning about top XML tag in simulation file

6 Feb 2021

• Fixed bug that was keeping the start_at_site option from working

4 Feb 2021

• Fixed occasional problem with grid sizes from make_apbs_inputs
• Updated documentation and behavior of coffdrop_chain. Now it will set never_frozen to false unless explicitly told otherwise.

2 Feb 2021

• nam_simulation was ignoring user-input n_output_states_per_block value.
• make_apbs_inputs was generating grid dimensions that were smaller than allowed by APBS.

27 Jan 2021

• Improved the algorithm used for rotations and constraints. This should improve performance and perhaps accuracy.
• Updated tutorial for Browndye 2.0

18 Jan 2021

• The tag min_rxn_dist_file was not getting propagated by bd_top to the simulation file.

8 Jan 2021

• Fixed some problems that were keeping it from compiling on newer versions of the Clang compiler and thus on the Mac

4 Jan 2021

• Fixed an inconsistency in bd_top which caused a mismatch between surface atom file names in the directory and in the simulation file.

30 Dec 2020

• Fixed bug in bd_top in which the original atom file for a core was being passed to the simulation file input to nam_simulation. Now the surface atoms are being passed correctly.
• Removed requirement for nam_simulation to check the sizes of the electrostatic grids generated by make_apbs_inputs.
• Removed requirement for a reaction file

23 Dec 2020

• Added extra size to innermost grids from make_apbs_input to avoid problems with other programs that use the grids
• Corrected documentation of make_apbs_input to include the solvent_radius tag in the solvent section

18 Dec 2020

• Added PQR output option to vtf_trajectory program
• Removed xyz_trajectory program

15 Dec 2020

• Fixed problem in make_apbs_inputs that would occasionally make grid dimensions which would make APBS complain

8 Dec 2020

• Fixed occasional convergence problem in constraint solver

6 Dec 2020

• Fixed bug in bd_top
• Added make_apbs_inputs and run_apbs_inputs, utilities for generating APBS grid specifications. Documentation is also added.
• Added alerts to unused XML tags in input to simulation programs

6 Nov 2020

• Added mailing list

28 Sep 2020

• Fixed bug in bd_top that was incorrectly computing grid bounds

24 Aug 2020

• Removed outdated reference to an external library

13 Apr 2020

• Fixed bug in parameter file parsing

9 Apr 2020

• Improved error reporting with XML parsing
• Fixed bug in hydrodynamic interactions

25 Mar 2020

• Fixed problems with constraints

20 Mar 2020

• Many bug fixes

16 Jan 2020

• Fixed bug in reading in COFFDROP parameter file

12 Dec 2019

• Added bond constraint option to coffdrop_chains
• Included better COFFDROP parameter file

19 Sep 2019

• Added the ability to use the Boost Filesystem library, in case the new C++ standard file library is missing, which seems to be the case for the Mac. See the top of the Makefile, or the updated browndye2.pdf, for instructions.
• Put error message in generate_coffdrop_beads to warn of residue names undefined in COFFDROP.

16 Sep 2019

• Now allowing hydrodynamics to be updated between several timesteps rather than at every step

10 Sep 2019

• Fixed annoying warning messages from clang++

28 Aug 2019

• Fixed some issues with the "no hydrodynamics" option

22 Aug 2019

• Added ability to turn off hydrodynamic interactions

13 Aug 2019

• Added bd_top and documentation for Browndye 2

25 Jul 2019

• Fixed some problems that might have slowed down trajectory output
• Added new setting to control trajectory output: n_output_states_per_block

24 Jul 2019

• Added program scale_interactions for scaling nonbonded COFFDROP interactions.

4 Jun 2019

• Fixed some bugs in generate_coffdrop_beads regarding handling of capping residues and terminal atoms
• Fixed parameter files to better handle capping and terminal residues
• Fixed missing dihedral potential in COFFDROP file

25 Apr 2019

• Many bug fixes

11 Mar 2019

• Fixed bug in generate_coffdrop_beads
• protein_test_charges now works with files of COFFDROP beads

19 Feb 2019

• Now the time is output by nam_simulation, and is displayed by process_trajectories.

23 Jan 2019

• bug fixes

16 Jan 2019

• Fixed problems with hydrodynamics
• Did some cleaning up of code

28 Nov 2018

• Fixed further bug in handling of capped residues; updated COFFDROP files

26 Nov 2018

• Fixed handling of capped residues in COFFDROP model

19 Nov 2018

• Fixed bug in coffdrop_chain

5 Nov 2018

• Simplified some of the code and fixed bugs

12 Sep 2018

• Updated the coffdrop_chain program to include attached cores

5 Sep 2018

• Fixed bug in generate_coffdrop_beads

28 Aug 2018

• Fixed bug in time step selector which was causing chains to blow up
• Fixed unwanted display of "improper" COFFDROP bonds in trajectories
• Fixed inconsistent initial centering of first group

1 Aug 2018

• Fixed obscure C++ weirdness that was preventing compilation on the Mac

23 July 2018

• Fixed bug in mrc2dx

20 July 2018

• Reaction file no longer required

17 July 2018

• fixed bug in mrc2dx program

2 July 2018

• added thrombin example (user-unfriendly version still)
• fixed some bugs