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)
Dawid Jagiela [Fri, 18 May 2012 11:53:24 +0000 (13:53 +0200)]
deleted: PARAM/1igd.cart~
Dawid Jagiela [Fri, 18 May 2012 11:24:20 +0000 (13:24 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Fri, 18 May 2012 11:23:42 +0000 (13:23 +0200)]
fixed ascii art frames in source/cluster/wham/src-M/energy_p_new.F
Cezary Czaplewski [Fri, 18 May 2012 11:17:38 +0000 (13:17 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Fri, 18 May 2012 11:16:06 +0000 (13:16 +0200)]
an example for MIN only version of unres, corrected paths in Makefile
Dawid Jagiela [Fri, 18 May 2012 11:13:14 +0000 (13:13 +0200)]
Merge branch 'feature-cmake' into devel
Dawid Jagiela [Fri, 18 May 2012 10:41:17 +0000 (12:41 +0200)]
another ascii art frame fix
Dawid Jagiela [Fri, 18 May 2012 10:08:31 +0000 (12:08 +0200)]
fix for gfortran build of source/cluster/unres
Dawid Jagiela [Wed, 16 May 2012 18:44:21 +0000 (20:44 +0200)]
fixed typo
Dawid Jagiela [Wed, 16 May 2012 18:33:49 +0000 (20:33 +0200)]
added CMake files to build cluster/wham/src-M
Dawid Jagiela [Tue, 15 May 2012 20:26:02 +0000 (22:26 +0200)]
added missig wham/src-M source files to cmake build
Dawid Jagiela [Tue, 15 May 2012 13:17:01 +0000 (15:17 +0200)]
Added CMake files for building source/wham/src-M
Dawid Jagiela [Mon, 14 May 2012 23:32:50 +0000 (01:32 +0200)]
ascii frames closed: unres/src_MD-M/energy_p_new_barrier.F
ascii frames closed: wham/src/energy_p_new.F
Dawid Jagiela [Mon, 14 May 2012 23:02:20 +0000 (01:02 +0200)]
1) ASCII art frame fix in unres/src_MD-M/energy_p_new_barrier.F
2) added gfortran build flags for wham/src
Dawid Jagiela [Mon, 14 May 2012 22:33:29 +0000 (00:33 +0200)]
added cmake files to build source/wham/src under ifort
Dawid Jagiela [Mon, 14 May 2012 15:02:00 +0000 (17:02 +0200)]
fixed more typos
Dawid Jagiela [Mon, 14 May 2012 13:53:46 +0000 (15:53 +0200)]
fixed typo
Dawid Jagiela [Mon, 14 May 2012 13:44:55 +0000 (15:44 +0200)]
prng_32.F/prng.f fix for intel compiler
Dawid Jagiela [Mon, 14 May 2012 13:16:23 +0000 (15:16 +0200)]
1) moved xdrf library to source/lib/xdrf - CMake files link this location when required by build binaries (Makefiles dont!)
2) added cmake files for building source/xdrfpdb/src and source/xdrfpdb/src-M
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
Dawid Jagiela [Sun, 13 May 2012 15:02:51 +0000 (17:02 +0200)]
linking pthreads for unres/src_MIN
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
Dawid Jagiela [Sat, 12 May 2012 21:31:00 +0000 (23:31 +0200)]
modified: energy_p_new_barrier.F - closed ascii art frames
modified: ../src_MD-M/together.F - changed imax to overcome aretmitic overflow bug in gfortran
Dawid Jagiela [Sat, 12 May 2012 21:10:42 +0000 (23:10 +0200)]
Additional MPI libraries search path added
Dawid Jagiela [Sat, 12 May 2012 13:11:10 +0000 (15:11 +0200)]
fix of production code that requires MPI
Dawid Jagiela [Fri, 11 May 2012 21:52:22 +0000 (23:52 +0200)]
added/modified CMake files for all subdirs in source/unres + junkfiles cleanup
Dawid Jagiela [Thu, 10 May 2012 21:47:23 +0000 (23:47 +0200)]
added piasek cluster specific compile conditioning in main cmake file
Dawid Jagiela [Thu, 10 May 2012 21:09:48 +0000 (23:09 +0200)]
closing asci-art frames in energy_p_new_barrier.F files removed some warnings in gfortran
Dawid Jagiela [Thu, 10 May 2012 20:21:12 +0000 (22:21 +0200)]
fixes for unres/src_MIN build in ifort
Dawid Jagiela [Thu, 10 May 2012 14:09:59 +0000 (16:09 +0200)]
- added UNRES Multichain examples
- CMake for src_MIN
- junkfiles cleanup
Dawid Jagiela [Thu, 10 May 2012 11:45:30 +0000 (13:45 +0200)]
added 32/64-bit architecture detection
Dawid Jagiela [Thu, 10 May 2012 10:02:22 +0000 (12:02 +0200)]
deleted: source/unres/src_MD-M/xdrf_em64/libxdrf.m4~
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
Dawid Jagiela [Wed, 9 May 2012 21:20:38 +0000 (23:20 +0200)]
src_MD-M CMake build files + junkfiles cleanup
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 [Tue, 8 May 2012 14:14:27 +0000 (16:14 +0200)]
deleted: CTestConfig.cmake
Dawid Jagiela [Tue, 8 May 2012 13:24:07 +0000 (15:24 +0200)]
fixed test_single_ala.sh to run binary from current build dir
Dawid Jagiela [Tue, 8 May 2012 13:20:18 +0000 (15:20 +0200)]
fixed "rm tmptmp" of notexisting file in compinfo.c
Dawid Jagiela [Tue, 8 May 2012 13:08:21 +0000 (15:08 +0200)]
fixed drop side on CTestConfig.cmake
Dawid Jagiela [Tue, 8 May 2012 11:53:44 +0000 (13:53 +0200)]
gfortran 4.5.2 (f95) compile definitions fix
Dawid Jagiela [Mon, 7 May 2012 13:41:42 +0000 (15:41 +0200)]
new gfortran fix
Dawid Jagiela [Mon, 7 May 2012 12:47:56 +0000 (14:47 +0200)]
fixed ctest/cmake files for src_MD build
Dawid Jagiela [Mon, 23 Apr 2012 11:41:40 +0000 (13:41 +0200)]
Added test MPI preprocessor compile definitions
Dawid Jagiela [Thu, 19 Apr 2012 22:54:26 +0000 (00:54 +0200)]
Revert "Revert "CMake file for xdrf library""
This reverts commit
4dd6545a13d055f8b951dd893270dc722212dd60.
Dawid Jagiela [Thu, 19 Apr 2012 22:52:59 +0000 (00:52 +0200)]
Revert "CMake file for xdrf library"
This reverts commit
154f05b81b221aecfb80de0cc515c23b65909c85.
Dawid Jagiela [Thu, 19 Apr 2012 22:49:41 +0000 (00:49 +0200)]
CMake file for xdrf library
Dawid Jagiela [Thu, 19 Apr 2012 14:25:10 +0000 (16:25 +0200)]
CMake project files added
Dawid Jagieła [Tue, 17 Apr 2012 12:50:54 +0000 (14:50 +0200)]
minor changes in Changelog
Dawid Jagieła [Tue, 17 Apr 2012 12:41:37 +0000 (14:41 +0200)]
Changelog entry time format changed to YYYY-MM-DD
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