Adam Kazimierz Sieradzan [Thu, 24 Jul 2014 14:22:58 +0000 (10:22 -0400)]
After long DEBUG of energy function
Dawid Jagiela [Wed, 23 Jul 2014 11:05:07 +0000 (13:05 +0200)]
added "make install" support for: unres (MD, MD-M, MIN) and maxlik
Adam Sieradzan [Tue, 22 Jul 2014 08:23:13 +0000 (10:23 +0200)]
correction in MD returnbox
Adam Kazimierz Sieradzan [Fri, 4 Jul 2014 18:40:17 +0000 (14:40 -0400)]
BUG FIX for SUMSL minimization
Adam Sieradzan [Tue, 24 Jun 2014 08:26:42 +0000 (10:26 +0200)]
bug fix for langevin dynamics
Conflicts:
.gitignore
source/unres/src_MD-M-newcorr/stochfric.F
Adam Sieradzan [Tue, 24 Jun 2014 08:41:41 +0000 (10:41 +0200)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Tue, 24 Jun 2014 08:26:42 +0000 (10:26 +0200)]
bug fix for langevin dynamics
Cezary Czaplewski [Tue, 24 Jun 2014 06:46:23 +0000 (08:46 +0200)]
Makefile without debuging
Cezary Czaplewski [Wed, 18 Jun 2014 12:56:05 +0000 (14:56 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Wed, 18 Jun 2014 12:53:25 +0000 (14:53 +0200)]
dyn-ss in MD-M
Adam Kazimierz Sieradzan [Tue, 17 Jun 2014 19:13:00 +0000 (15:13 -0400)]
dalej wylaczona diagnostyka
Adam Kazimierz Sieradzan [Tue, 17 Jun 2014 18:18:21 +0000 (14:18 -0400)]
wylacznie diagnostyki
Adam Kazimierz Sieradzan [Tue, 17 Jun 2014 18:13:35 +0000 (14:13 -0400)]
doadany sccor_am1 do PBC (needs veryfy)
Cezary Czaplewski [Tue, 17 Jun 2014 11:18:05 +0000 (13:18 +0200)]
correcter Makefile and errors side chain parameters
Cezary Czaplewski [Tue, 17 Jun 2014 09:42:27 +0000 (11:42 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Tue, 17 Jun 2014 09:34:30 +0000 (11:34 +0200)]
xdrf2x tests
Adam Sieradzan [Thu, 12 Jun 2014 09:21:36 +0000 (11:21 +0200)]
compiling cluster before tests
Adam Sieradzan [Tue, 10 Jun 2014 16:03:57 +0000 (18:03 +0200)]
Introduction of PBC to cluster energy and reading, turn off wham one of the debug
Adam Sieradzan [Tue, 10 Jun 2014 14:54:54 +0000 (16:54 +0200)]
Bug fix for reading single residue from pdb
Dawid Jagieła [Tue, 3 Jun 2014 15:35:28 +0000 (17:35 +0200)]
fixed typo
Dawid Jagieła [Tue, 3 Jun 2014 15:16:39 +0000 (17:16 +0200)]
fix for MD tests in E0LL2Y FF
Dawid Jagieła [Tue, 3 Jun 2014 11:57:14 +0000 (13:57 +0200)]
fixed binary name generation in unres/src_MD-M
Dawid Jagieła [Tue, 3 Jun 2014 11:54:04 +0000 (13:54 +0200)]
kolejne porzadki
Dawid Jagieła [Tue, 3 Jun 2014 11:48:09 +0000 (13:48 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagieła [Tue, 3 Jun 2014 11:47:06 +0000 (13:47 +0200)]
wywalka smieci - ludzie budujcie w katalogu build!
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:18:28 +0000 (13:18 +0200)]
Merge branch 'devel' of mmka:unres into devel
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:16:30 +0000 (13:16 +0200)]
New CMake files after cleaning
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:13:06 +0000 (13:13 +0200)]
Modification files required corresponding architecture
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:11:13 +0000 (13:11 +0200)]
Modification files required corresponding architecture
Adam Sieradzan [Sun, 25 May 2014 15:25:16 +0000 (17:25 +0200)]
zmiany w multichainie
Adam Kazimierz Sieradzan [Sun, 25 May 2014 15:23:08 +0000 (11:23 -0400)]
zmiany, wylaczenie diagnostyki, dzialajacy WHAM
Adam Kazimierz Sieradzan [Wed, 21 May 2014 11:43:27 +0000 (07:43 -0400)]
diagnoza dlaczego WHAM nie dziala
Adam Kazimierz Sieradzan [Thu, 15 May 2014 07:53:58 +0000 (03:53 -0400)]
zmiany w WHAM PBC przed sprawdzeniem differow
Adam Sieradzan [Tue, 13 May 2014 10:05:51 +0000 (12:05 +0200)]
Wylacznie timiningu i sprawdzenie gradientu
Adam Sieradzan [Mon, 12 May 2014 17:15:54 +0000 (19:15 +0200)]
po przyspieszeniu przed checkgradem i sympcheckiem
Adam Sieradzan [Thu, 8 May 2014 15:36:52 +0000 (17:36 +0200)]
wlaczenie timing
Adam Sieradzan [Thu, 8 May 2014 15:25:43 +0000 (17:25 +0200)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Thu, 8 May 2014 15:25:03 +0000 (17:25 +0200)]
Adjusted energy file (small improvement)
Adam Sieradzan [Thu, 1 May 2014 18:52:58 +0000 (20:52 +0200)]
polepszenie wydajnosci algorytmu PBC
Dawid Jagiela [Fri, 25 Apr 2014 07:54:20 +0000 (03:54 -0400)]
1) added warnings suppression if find_package(MPI) failes to find MPI
2) removed non-standardold MPI paths - should be passed by cmake variables directly
Dawid Jagiela [Fri, 25 Apr 2014 07:54:20 +0000 (03:54 -0400)]
1) added warnings suppression if find_package(MPI) failes to find MPI
2) removed non-standardold MPI paths - should be passed by cmake variables directly
Dawid Jagieła [Tue, 15 Apr 2014 11:31:34 +0000 (13:31 +0200)]
DON'T DELETE THE "git-daemon-export-ok" FILE!!!
This file is mandatory for proper git-deamon work - without it you cannot access the repository using the git protocol "git://"
Adam Liwo [Thu, 10 Apr 2014 19:57:52 +0000 (15:57 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
Adam Liwo [Thu, 10 Apr 2014 18:28:20 +0000 (14:28 -0400)]
Added new files to the NEWCORR version
Adam Liwo [Thu, 10 Apr 2014 18:24:39 +0000 (14:24 -0400)]
Added source/wham/src-NEWSC-NEWCORR/
Adam Liwo [Thu, 10 Apr 2014 11:57:44 +0000 (07:57 -0400)]
Added src_MD-M-newcorr (Adasko's source) and src-NEWSC of WHAM (with Momo's SCSC potentials)
Adam Liwo [Tue, 1 Apr 2014 04:37:15 +0000 (00:37 -0400)]
Added src_Eshel (decoy processing for threading)
Adam Liwo [Wed, 19 Mar 2014 08:06:29 +0000 (04:06 -0400)]
Fixed iatsc_s and iatscp_s for 1 residue (was 0 with MPI version)
Adam Sieradzan [Tue, 18 Mar 2014 07:21:27 +0000 (08:21 +0100)]
Devel ma zle COMMON.TORSIONAL w src_MD (single chain)
Adam Sieradzan [Tue, 4 Mar 2014 11:32:18 +0000 (12:32 +0100)]
ignorowanie build theta
Adam Sieradzan [Mon, 3 Mar 2014 05:12:50 +0000 (06:12 +0100)]
poprawka w refsysie
Adam Sieradzan [Mon, 24 Feb 2014 19:23:03 +0000 (20:23 +0100)]
Working gradient for PBC
Adam Sieradzan [Thu, 20 Feb 2014 08:37:49 +0000 (09:37 +0100)]
Drobne zmiany i dodanei parametrow dla dummy atom
Adam Sieradzan [Mon, 17 Feb 2014 18:27:57 +0000 (19:27 +0100)]
The wrong one gradient compontent...
cleaning in progress by A.Liwo other gradient OK
Adam Sieradzan [Sat, 8 Feb 2014 17:27:39 +0000 (18:27 +0100)]
zmiany w galezi multichain
Adam Sieradzan [Wed, 29 Jan 2014 20:48:46 +0000 (21:48 +0100)]
DO zmiany czytanie pisanie i cutoff
Pawel Krupa [Wed, 20 Nov 2013 15:57:39 +0000 (10:57 -0500)]
Poprawione przyklady w polu ff_gab (zmieniony potencjal SIDEPAR na:
sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k).
Pawel Krupa [Wed, 20 Nov 2013 15:53:22 +0000 (10:53 -0500)]
Poprawione przyklady do pola ff_gab (zmieniony potencjal SIDEPAR na: sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k).
Adam Sieradzan [Mon, 18 Nov 2013 19:02:48 +0000 (20:02 +0100)]
dzialajacy gradient
Adam Sieradzan [Thu, 14 Nov 2013 22:25:51 +0000 (23:25 +0100)]
Dzialajacy gradient dla reszt 13 i 7
Adam Sieradzan [Thu, 14 Nov 2013 13:32:27 +0000 (14:32 +0100)]
zabezpieczenie przedczarkowe
Dawid Jagiela [Wed, 6 Nov 2013 10:01:12 +0000 (11:01 +0100)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Wed, 6 Nov 2013 10:00:38 +0000 (11:00 +0100)]
junk files cleanup
Adam Sieradzan [Tue, 5 Nov 2013 22:44:36 +0000 (23:44 +0100)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Tue, 5 Nov 2013 22:32:58 +0000 (23:32 +0100)]
Bugfix for smaller size of memory
Dawid Jagiela [Tue, 5 Nov 2013 20:45:53 +0000 (21:45 +0100)]
deleted: cluster/wham/src-M/permut.o
Adam Sieradzan [Tue, 5 Nov 2013 20:10:47 +0000 (21:10 +0100)]
Debug part 11
Adam Sieradzan [Tue, 5 Nov 2013 20:02:11 +0000 (21:02 +0100)]
Debug part 10
Adam Sieradzan [Tue, 5 Nov 2013 19:42:53 +0000 (20:42 +0100)]
Debug part 9
Adam Sieradzan [Tue, 5 Nov 2013 19:30:19 +0000 (20:30 +0100)]
Debug part 8
Adam Sieradzan [Tue, 5 Nov 2013 19:07:23 +0000 (20:07 +0100)]
Debug cd 7
Adam Sieradzan [Tue, 5 Nov 2013 18:35:49 +0000 (19:35 +0100)]
Debug part 7
Adam Sieradzan [Tue, 5 Nov 2013 18:02:35 +0000 (19:02 +0100)]
Debug part 6
Adam Sieradzan [Tue, 5 Nov 2013 17:49:55 +0000 (18:49 +0100)]
Debug part 5
Adam Sieradzan [Tue, 5 Nov 2013 17:30:04 +0000 (18:30 +0100)]
Debug part 4
Adam Sieradzan [Tue, 5 Nov 2013 17:24:58 +0000 (18:24 +0100)]
Debug part 3
Adam Sieradzan [Tue, 5 Nov 2013 17:04:35 +0000 (18:04 +0100)]
Debug part 2
Adam Sieradzan [Tue, 5 Nov 2013 16:30:27 +0000 (17:30 +0100)]
Debug part 1
Adam Sieradzan [Tue, 5 Nov 2013 13:51:57 +0000 (14:51 +0100)]
Merge branch 'adasko' into devel
Conflicts:
source/unres/src_MD/Makefile
Adam Sieradzan [Tue, 5 Nov 2013 13:39:58 +0000 (14:39 +0100)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Tue, 5 Nov 2013 13:39:29 +0000 (14:39 +0100)]
ignorowanie build2
Adam Sieradzan [Tue, 5 Nov 2013 13:37:15 +0000 (14:37 +0100)]
pierwsza proba merga devela do adasko
Merge branch 'devel' into adasko
Conflicts:
.gitignore
PARAM/pot_theta_G631_DIL.parm
PARAM/pot_theta_G631_DIL_ext.parm
bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
bin/unres_clustMD_MPI-oldparm
bin/wham/wham_multparm-ham_rep-oldparm
source/cluster/wham/src-M/CMakeLists.txt
source/cluster/wham/src-M/COMMON.SCCOR
source/cluster/wham/src-M/cartprint.o
source/cluster/wham/src-M/chainbuild.o
source/cluster/wham/src-M/contact.o
source/cluster/wham/src-M/convert.o
source/cluster/wham/src-M/energy_p_new.o
source/cluster/wham/src-M/geomout.o
source/cluster/wham/src-M/hc.o
source/cluster/wham/src-M/initialize_p.o
source/cluster/wham/src-M/int_from_cart1.o
source/cluster/wham/src-M/main_clust.o
source/cluster/wham/src-M/parmread.o
source/cluster/wham/src-M/permut.o
source/cluster/wham/src-M/proc_proc.o
source/cluster/wham/src-M/read_coords.o
source/cluster/wham/src-M/read_ref_str.o
source/cluster/wham/src-M/readpdb.o
source/cluster/wham/src-M/readrtns.o
source/cluster/wham/src-M/rescode.o
source/cluster/wham/src-M/setup_var.o
source/cluster/wham/src-M/wrtclust.o
source/cluster/wham/src-M/xdrf/libxdrf.a
source/cluster/wham/src/energy_p_new.F
source/unres/src_MD-M/COMMON.SCCOR
source/unres/src_MD-M/COMMON.TORSION
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/cinfo.f
source/unres/src_MD-M/stochfric.F
source/unres/src_MD/COMMON.LOCAL
source/unres/src_MD/COMMON.SCCOR
source/unres/src_MD/Makefile
source/unres/src_MD/cinfo.f
source/unres/src_MD/parmread.F
source/wham/src-M/CMakeLists.txt
source/wham/src-M/cinfo.f
source/wham/src-M/include_unres/COMMON.SCCOR
source/wham/src/Makefile
source/wham/src/cinfo.f
source/wham/src/enecalc1.F
source/wham/src/energy_p_new.F
source/wham/src/include_unres/COMMON.SCCOR
source/wham/src/int_from_cart.f
source/wham/src/parmread.F
Adam Sieradzan [Tue, 5 Nov 2013 13:15:27 +0000 (14:15 +0100)]
Dostosowanie w src whama i clustra
Adam Sieradzan [Tue, 5 Nov 2013 07:15:34 +0000 (08:15 +0100)]
Merge branch 'adasko' of mmka:unres into adasko
Cezary Czaplewski [Wed, 30 Oct 2013 20:51:11 +0000 (21:51 +0100)]
Makefile for pgi 2013
Cezary Czaplewski [Wed, 30 Oct 2013 18:33:20 +0000 (19:33 +0100)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Wed, 30 Oct 2013 18:31:24 +0000 (19:31 +0100)]
testing Makefile for pgi compiler
Adam Sieradzan [Wed, 16 Oct 2013 13:51:06 +0000 (15:51 +0200)]
drobnostki w ext theta (cofniete)
Adam Sieradzan [Mon, 7 Oct 2013 17:45:58 +0000 (19:45 +0200)]
small correctian in wham
Dawid Jagiela [Sun, 22 Sep 2013 13:26:40 +0000 (15:26 +0200)]
show_UNRES.py - large loops speedup by using xrange
Dawid Jagiela [Mon, 2 Sep 2013 15:06:12 +0000 (17:06 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Mon, 2 Sep 2013 15:05:23 +0000 (17:05 +0200)]
resolved conflicts in: source/unres/src_MD/CMakeLists.txt
Cezary Czaplewski [Mon, 2 Sep 2013 15:04:07 +0000 (17:04 +0200)]
repair of broken merge
Cezary Czaplewski [Mon, 2 Sep 2013 13:20:28 +0000 (15:20 +0200)]
Merge branch 'devel' of mmka:unres into devel
Conflicts:
source/unres/src_MD/CMakeLists.txt
Cezary Czaplewski [Mon, 2 Sep 2013 13:18:05 +0000 (15:18 +0200)]
merging devel
Cezary Czaplewski [Mon, 2 Sep 2013 13:02:33 +0000 (15:02 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Mon, 2 Sep 2013 13:01:15 +0000 (15:01 +0200)]
dynamic disulfides in multichain
Adam Kazimierz Sieradzan [Mon, 2 Sep 2013 12:21:17 +0000 (08:21 -0400)]
Zmiany w pliku sccor_am1_pawel.dat
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 19:08:38 +0000 (15:08 -0400)]
1)Clean-up 2)making similar src_MD and its multichain version 3)
correction of potentials and bugfix in ../PARAM/pot_theta_G631_DIL.parm
4) introduction of theta_pdb and rotam_pdb in multichain
Dawid Jagiela [Sat, 31 Aug 2013 18:35:42 +0000 (20:35 +0200)]
Merge branch 'devel' of mmka:unres into devel
projects / unres.git / log