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Adam Liwo [Mon, 18 Jun 2012 13:58:32 +0000 (09:58 -0400)]
Merge branch 'adam' into devel
Merging adam with devel
Conflicts:
source/unres/src_CSA/readrtns_csa.F
Adam Liwo [Fri, 15 Jun 2012 19:09:20 +0000 (15:09 -0400)]
6/15/2012 by Adam
Minor changes; linked parallal Makefile in CSA
Adam Liwo [Thu, 14 Jun 2012 20:20:40 +0000 (16:20 -0400)]
6/14/12 by Adam: unnecessary files deleted
Adam Liwo [Thu, 14 Jun 2012 20:16:07 +0000 (16:16 -0400)]
6/14/12 by Adam - changes committed
Adam Liwo [Thu, 14 Jun 2012 20:10:25 +0000 (16:10 -0400)]
6/14/2012 by Adam
1. Fixed a bug in the minimization in angles im all versions; varia
was a simple variable in the calling and a vector in the called subroutine.
2. Removed (wrong) temperature scaling in the CSA snd in the MD version.
3. Added selection of printout information in SUMSL.
Adam Liwo [Mon, 11 Jun 2012 14:43:15 +0000 (10:43 -0400)]
6/11/2012 by Adam
Yet another revision of xdrf2pdb-m. Error detected in description; directory src-M all pertains to
multi-chain systems (but the programs can also be used for single-chain systems). xdrf2pdb-m for
single-chain systems is in src
Adam Liwo [Mon, 11 Jun 2012 14:25:25 +0000 (10:25 -0400)]
6/11/2012 by Adam
xdrf-m corrected (list of arguments); changes in manual required!
Cezary Czaplewski [Wed, 9 May 2012 12:02:13 +0000 (14:02 +0200)]
DFA is switched off by default
Adam Liwo [Mon, 11 Jun 2012 11:07:18 +0000 (07:07 -0400)]
6/11/2012 Changes of the CSA version
Adam Liwo [Mon, 11 Jun 2012 11:06:28 +0000 (07:06 -0400)]
6/11/2012 Update of the CSA version
Adam Liwo [Tue, 29 May 2012 08:52:17 +0000 (04:52 -0400)]
5/29/2012 by Adam
1. Fixed NaNs in wham (more stable computation of window free energies).
2. Minor fixes in cluster
3. Added exmaple with minimization in MD examples
Adam Liwo [Sun, 20 May 2012 11:33:15 +0000 (07:33 -0400)]
5/20/2012 by Adam
1. Added distance restraints to wham and cluster
2. Fixed the bug in angle restraints to wham and added angle restraints to cluster
3. Introduced more stable procedure to calculate the dependence of ensemble averages on temperature in wham (for each temperature the lowest "free energy" is a reference to compute Boltzmann factors)
Adam Liwo [Sun, 13 May 2012 20:10:21 +0000 (16:10 -0400)]
5/13/2012 by Adam
Minor bugs in the code related to distance restraints fixed: readrtns.F
Adam Liwo [Sun, 13 May 2012 06:16:52 +0000 (02:16 -0400)]
5/13/2012 by Adam
1. Added options to run simulations with NMR-type distance restraints;
introduced array dhpb1 to store right borders of distance restraints
(left borders stored in dhpb, if dhpb1(i).eq.0 ith restraint is harmonic type,
> 0, quartic (NMR-like) type).
2. Added option to imposed either Calpha or SC (Cbeta) restraints; the pertinent
array is ibecacarb.
3. The above changes have been introduced in readrtns.F and energy_p_new_barrier.F
Cleaned excessive output in MREMD.F (energies at exchange)
4. prng.f replaces prng_32.F in Intel Makefiles; program hangs up with prng_32
Adam Liwo [Thu, 10 May 2012 05:30:53 +0000 (01:30 -0400)]
5/10/2012 by Adam
1. Added C-shell scripts for the GAB and E0LL2Y force field
2. Added examples for multichain calculations
Cezary Czaplewski [Wed, 9 May 2012 12:21:21 +0000 (14:21 +0200)]
compilation of DFA/CSA code
Cezary Czaplewski [Wed, 9 May 2012 12:05:03 +0000 (14:05 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Wed, 9 May 2012 12:02:13 +0000 (14:02 +0200)]
DFA is switched off by default
Dawid Jagiela [Thu, 19 Apr 2012 14:25:10 +0000 (16:25 +0200)]
CMake project files added
Cezary Czaplewski [Wed, 11 Apr 2012 20:46:25 +0000 (22:46 +0200)]
minimization in csa code is working now correctly
Cezary Czaplewski [Wed, 4 Apr 2012 09:10:17 +0000 (11:10 +0200)]
tag updated to v.3.1
Dawid Jagieła [Tue, 3 Apr 2012 13:58:42 +0000 (15:58 +0200)]
updated Changelog
Dawid Jagieła [Tue, 3 Apr 2012 13:47:19 +0000 (15:47 +0200)]
Added Changelog
Adam Liwo [Mon, 2 Apr 2012 12:31:28 +0000 (08:31 -0400)]
New files added
Adam Liwo [Mon, 2 Apr 2012 12:29:33 +0000 (08:29 -0400)]
Makefiles for specific compilers and force fields created
Adam Liwo [Thu, 29 Mar 2012 13:20:38 +0000 (09:20 -0400)]
Added example files (1L2Y)
Adam Liwo [Thu, 29 Mar 2012 13:15:50 +0000 (09:15 -0400)]
Example input files for 1L2Y added
Adam Liwo [Thu, 29 Mar 2012 13:01:13 +0000 (09:01 -0400)]
Unnecessary object files removed
Adam Liwo [Thu, 29 Mar 2012 12:50:23 +0000 (08:50 -0400)]
Makefile_single_gfortran_oldparm corrected to include new directory structure
Cezary Czaplewski [Wed, 28 Mar 2012 22:33:41 +0000 (00:33 +0200)]
path for executable corrected
Cezary Czaplewski [Wed, 28 Mar 2012 22:17:43 +0000 (00:17 +0200)]
compilation of new CSA version
Cezary Czaplewski [Wed, 28 Mar 2012 21:55:24 +0000 (23:55 +0200)]
new files for tmscore and reminimization
Cezary Czaplewski [Wed, 28 Mar 2012 21:53:42 +0000 (23:53 +0200)]
cleaning - unecessary files deleted
tmscore has been added to CSA as alternative of angular difference
reminimization is working in CSA version
Cezary Czaplewski [Wed, 28 Mar 2012 21:39:50 +0000 (23:39 +0200)]
final changes to remove CSA from MD version of the code
new executable
Cezary Czaplewski [Wed, 28 Mar 2012 21:36:06 +0000 (23:36 +0200)]
removal of CSA from MD version of code
backup *~ files deleted
other minor changes in the code
Cezary Czaplewski [Wed, 28 Mar 2012 21:06:45 +0000 (23:06 +0200)]
old unecessary files are deleted
Adam Liwo [Wed, 21 Mar 2012 13:08:53 +0000 (14:08 +0100)]
xdrf2pdb-M.F: corrected order of reading
Adam Liwo [Wed, 21 Mar 2012 13:06:31 +0000 (14:06 +0100)]
plik1 deleted by Adam
Dawid Jagieła [Wed, 21 Mar 2012 08:41:55 +0000 (09:41 +0100)]
dodalem pusty plik
Dawid Jagieła [Sat, 25 Feb 2012 12:55:23 +0000 (13:55 +0100)]
added source code