Adam Kazimierz Sieradzan [Thu, 11 Sep 2014 19:14:53 +0000 (15:14 -0400)]
poprawka w triss
Adam Kazimierz Sieradzan [Thu, 24 Jul 2014 14:22:58 +0000 (10:22 -0400)]
After long DEBUG of energy function
Adam Sieradzan [Tue, 22 Jul 2014 08:23:13 +0000 (10:23 +0200)]
correction in MD returnbox
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 Kazimierz Sieradzan [Tue, 17 Jun 2014 18:13:35 +0000 (14:13 -0400)]
doadany sccor_am1 do PBC (needs veryfy)
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
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 15:25:03 +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
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
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 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)
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
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
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 12:58:46 +0000 (08:58 -0400)]
Merge branch 'adasko' of mmka.chem.univ.gda.pl:unres into adasko
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 12:41:51 +0000 (08:41 -0400)]
Merge mmka.chem.univ.gda.pl:unres into adasko
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 12:22:46 +0000 (08:22 -0400)]
Clean-up in parmread for src-MD and src-MD-M
pre-preparation for removal of src-MD and leaving out only the
multichain version
Dawid Jagiela [Fri, 23 Aug 2013 12:11:37 +0000 (14:11 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Fri, 23 Aug 2013 09:58:30 +0000 (11:58 +0200)]
Fix to use native system xdr headers
Signed-off-by: Dawid Jagiela <lightnir@chem.univ.gda.pl>
Adam Sieradzan [Mon, 12 Aug 2013 20:32:43 +0000 (22:32 +0200)]
new tosrional double torsional and valence
Adam Sieradzan [Mon, 12 Aug 2013 20:32:43 +0000 (22:32 +0200)]
new tosrional double torsional and valence
Dawid Jagiela [Thu, 25 Jul 2013 08:53:59 +0000 (10:53 +0200)]
test name changed for unres MD DFA version
Dawid Jagiela [Thu, 25 Jul 2013 08:53:59 +0000 (10:53 +0200)]
test name changed for unres MD DFA version
Dawid Jagiela [Thu, 25 Jul 2013 08:35:26 +0000 (10:35 +0200)]
Merge branch 'prerelease-3.2.1' into devel
Dawid Jagiela [Thu, 25 Jul 2013 08:35:26 +0000 (10:35 +0200)]
Merge branch 'prerelease-3.2.1' into devel
Dawid Jagiela [Thu, 25 Jul 2013 08:14:18 +0000 (10:14 +0200)]
fixed WHAM for gfortran: src/energy_p_new.F
Dawid Jagiela [Thu, 25 Jul 2013 08:14:18 +0000 (10:14 +0200)]
fixed WHAM for gfortran: src/energy_p_new.F
Adam Sieradzan [Tue, 16 Jul 2013 19:01:25 +0000 (21:01 +0200)]
NIE PEWNE ZMIANY ZWERYFIKUJ!!
Adam Kazimierz Sieradzan [Fri, 28 Jun 2013 18:12:54 +0000 (14:12 -0400)]
Just few comments added to WHAM to clarify
Adam Kazimierz Sieradzan [Fri, 28 Jun 2013 18:12:54 +0000 (14:12 -0400)]
Just few comments added to WHAM to clarify
Adam Kazimierz Sieradzan [Fri, 28 Jun 2013 01:00:10 +0000 (21:00 -0400)]
Bugfix for SS wham and introduction SS to cluster analysis
Adam Kazimierz Sieradzan [Fri, 28 Jun 2013 01:00:10 +0000 (21:00 -0400)]
Bugfix for SS wham and introduction SS to cluster analysis
Adam Kazimierz Sieradzan [Tue, 25 Jun 2013 23:37:52 +0000 (19:37 -0400)]
Dodanie dynamic disulfide to WHAM
Adam Kazimierz Sieradzan [Tue, 25 Jun 2013 23:37:52 +0000 (19:37 -0400)]
Dodanie dynamic disulfide to WHAM
Cezary Czaplewski [Tue, 7 May 2013 13:39:45 +0000 (15:39 +0200)]
some corrections in xdrf2pdb-m for dyn_ss
Cezary Czaplewski [Tue, 7 May 2013 13:39:45 +0000 (15:39 +0200)]
some corrections in xdrf2pdb-m for dyn_ss
Cezary Czaplewski [Tue, 30 Apr 2013 07:10:32 +0000 (09:10 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Tue, 30 Apr 2013 07:10:32 +0000 (09:10 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Tue, 30 Apr 2013 07:08:54 +0000 (09:08 +0200)]
testing ssbond in cx
Cezary Czaplewski [Tue, 30 Apr 2013 07:08:54 +0000 (09:08 +0200)]
testing ssbond in cx
Dawid Jagiela [Thu, 18 Apr 2013 14:44:24 +0000 (16:44 +0200)]
restructured examples
Dawid Jagiela [Thu, 18 Apr 2013 14:44:24 +0000 (16:44 +0200)]
restructured examples
Dawid Jagiela [Mon, 15 Apr 2013 11:38:26 +0000 (13:38 +0200)]
changed SCCORPAR to shelly potentials in GAB & 12LY ff - UNRESInpGen.py
Dawid Jagiela [Mon, 15 Apr 2013 11:38:26 +0000 (13:38 +0200)]
changed SCCORPAR to shelly potentials in GAB & 12LY ff - UNRESInpGen.py
Dawid Jagiela [Fri, 12 Apr 2013 10:47:11 +0000 (12:47 +0200)]
added default preprocessor flags for unknown compilers
Dawid Jagiela [Fri, 12 Apr 2013 10:47:11 +0000 (12:47 +0200)]
added default preprocessor flags for unknown compilers
Dawid Jagiela [Thu, 11 Apr 2013 11:17:48 +0000 (13:17 +0200)]
added REMD/MREMD input generation in UNRESInpGen.py
Dawid Jagiela [Thu, 11 Apr 2013 11:17:48 +0000 (13:17 +0200)]
added REMD/MREMD input generation in UNRESInpGen.py
Cezary Czaplewski [Mon, 8 Apr 2013 13:01:54 +0000 (09:01 -0400)]
correct writing of dyn_ss for cx and x
Cezary Czaplewski [Mon, 8 Apr 2013 13:01:54 +0000 (09:01 -0400)]
correct writing of dyn_ss for cx and x
Dawid Jagiela [Thu, 7 Mar 2013 12:10:51 +0000 (13:10 +0100)]
added OVERLAP and NOSEARCHSC options in UNRESInpGen.py
Dawid Jagiela [Thu, 7 Mar 2013 12:10:51 +0000 (13:10 +0100)]
added OVERLAP and NOSEARCHSC options in UNRESInpGen.py
Dawid Jagiela [Wed, 6 Mar 2013 15:26:08 +0000 (16:26 +0100)]
Added minimazation support to UNRESInpGen.py
Dawid Jagiela [Wed, 6 Mar 2013 15:26:08 +0000 (16:26 +0100)]
Added minimazation support to UNRESInpGen.py
Dawid Jagiela [Tue, 5 Mar 2013 11:32:20 +0000 (12:32 +0100)]
added glicyne support in show_UNRES.py
Dawid Jagiela [Tue, 5 Mar 2013 11:32:20 +0000 (12:32 +0100)]
added glicyne support in show_UNRES.py
projects / unres.git / log