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qgui_history
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23.08.16 v2.53
Added option to select nucleic acids in analyse RMSF/RMSD.
06.07.16 v2.52
Added error handling to Analyze FEP module to deal with crashed simulations.
Fixed issue with trjmask module resulting from long file names/paths.
Fixed unlikely issue in trjmask module if user selects duplicate file name.
09.06.12 v2.51
Nasty fix for a nasty mistake:
Fixed critical issue in EVB setup that appears when a bond is
off (0) in all states resulting in bonds/angles/torsion ignoring
this completely when generating the FEP file.
07.06.16 v2.5
Added tool to create a pdb file based on the trajectory atom mask,
for when there is a mismatch between topology and trajectory atoms.
19.05.16 v2.4
Changed the work routine of autogenerating EVB parameters from
template structures that used to be completely automatically
created from pymol. Now it is a 2-step thing where the user can
in round 1 control and edit the template strcutres before in round 2
writing them to disk an using them in ffld_server.
12.05.16 v2.31
Improved auto evb parameter generation tool when generating template
structures: imrpoved pymol seleciton string for h_add.
10.05.16 v2.3
Added option to write PDB file in the parameter generation tool. This
is to generate a .mae file from the pdb file with correct bond-orders
and formal charges. Makes it easier to get correct parameters.
29.04.16 v2.2
*Removed OPLS-2001 from selectable parameterlist since it is not
possible to use it in shcrodinger ffld_server anymore.
*Minor improvements to the removal of outliers in EVB arrhenius.
21.03.16 v2.1
Added functionality to the EVB Arrhenius class. Outliers can be
removed and the effect on the thermodynamic activation parameters
are updated accordingly.
15.03.16 v2.09
Fixed a problem with autogenerating disulfid-bridges in topology
prepare.
25.01.16 v2.08
Updated Qgui to changed Qfep output format in newest versions.
22.01.16 v2.071
Fixed analyze LIE problem to locate correct log files. The problem
is due to new header in the log files written by the latest Qdyn
versions.
21.01.16 v2.07
Added missing parameters in OPLS-2015 for water model required for
SHAKE in Q. Minor fixes to te EVB arrhenius class.
13.01.16 v2.06
Improved error handling for the EVB thermodynamic parameters class.
12.01.16 v2.05
Fixed improper sequnce of atoms error in EVB setup that is different
defined between OPLS and CHARMM FF.
08.01.16 v2.04
Fixed a latex title error for subscripts in the Analyze evb reaction
energies plotting of the reaction free energy profiles.
16.12.15 v2.03
Fixed Topology prepare 'toggle charge' function bug that prevented
removal of atoms as (user) defined in the '[toggle_residues]' in .lib.
Qoplsaa.lib and Qopls_2015.lib updated with some bug corrections.
23.11.15 v2.02
Fixed weird problem with converting string to integer in edit_evb.py.
20.11.15 v2.02
Fixed error caused when no toggle_residue defined in lib.
15.11.15 v2.01b
Bug fixes and minor improvements to the Topology prepare tool.
Removed 'return' statement that hindered the topology input files
to be written.
06.11.15 v2.0b
Complete remake of the topology prepare tool. This is now independent of
forcefield type, and residues that are togglable are defined directly in
the library file. Topology prepare now also syncs with PyMOL.
18.09.15 v1.2.0
Added the long time missing option to load a old FEP file
in the EVB setup. So now you do not have to redefine everything
when using the same topology.
03.08.15 v1.1.4
Improved bugs with the Analyze energies tool.
20.01.15 v1.1.3b
Fixed Qfep input generation in Analyze FEP so that ene files
are written from lambda = 1 to lambda = 0
Qfep is also set to run even if qfep.out already exists (this
is different from EVB).
14.01.15 v1.1.3
Fixed FEP softcore number syncing error
When using softcore, all Q atoms have to be defined. Automated.
07.01.15 version 1.1.2
Fixed 'Recompute EVB' error in Analyze EVB Thermodynamic Parameters
02.01.15 version 1.1.1
Improved x-labeling for plot in Analyze EVB Thermodynamic Parameters
25.12.14 version 1.1.0
Brand new tool available in the Analyze EVB Reaction Energies
- Fit Marcus parabolas to the diabatic free energy functions
- Compute the (intrinsic) reorganization energies
- Visualize the diabatic state functions and the adiabatic
mixing with and without the eigenvector coeffecients
22.12.14 version 1.0.7b
Fixed normalization bug of EVB reaction free energy profiles
when recomputing EVB in Analyze EVB Reaction Energies.
18.12.14 version 1.0.7
Launching Qgui with -p automatically sets the workdir to the
current directory.
Minor bug fixes to FEP parameter assignment routine.
16.12.14 version 1.0.6
Fixed handling of non-standard pdb atom names when communicating
with pymol in Qpymol and FEP setup
14.12.14 version 1.0.5b
Improved auto-generation of pymol template structures used for
ffld_server in FEP setup
09.12.14 version 1.0.5
Added state dependent el_scale for EVB setup.
Major improvement to autoassignment of parameters in FEP setup
13.10.14 version 1.0.4
User dependent settings are now stored independent of Qgui code
in $USER home directory (.qgui)
09.04.14 version 1.0.2b
New standar error estimation implemented for Analyze LIE.
(statistical inefficiency. s = lim [tb<E>b/<E>]
07.04.14 version 1.0.1b
+Changed fine tune search funciton in EVB RRC to
check [dG(act) - dG(rxn)] when tuning Hij. Old version
checked only dG(rxn) when fine tuning Hij.