Adam Sieradzan [Wed, 21 Oct 2015 16:13:45 +0000 (18:13 +0200)]
sprawdzenie shieldingu
Adam Sieradzan [Mon, 12 Oct 2015 09:11:08 +0000 (11:11 +0200)]
debug off
Adam Sieradzan [Tue, 29 Sep 2015 17:54:56 +0000 (19:54 +0200)]
Merge branch 'lipid' into AFM
Conflicts:
source/wham/src-M/DIMENSIONS.ZSCOPT
source/wham/src-M/energy_p_new.F
source/wham/src-M/initialize_p.F
source/wham/src-M/parmread.F
Adam Sieradzan [Tue, 29 Sep 2015 17:48:56 +0000 (19:48 +0200)]
ESSENTIAL CHANGE - BUG FIX in ENERGY to have old Correlation
Adam Sieradzan [Tue, 29 Sep 2015 11:02:05 +0000 (13:02 +0200)]
wham in lipid still diff
Adam Sieradzan [Tue, 29 Sep 2015 06:14:30 +0000 (08:14 +0200)]
modified lipid parm
Adam Sieradzan [Wed, 23 Sep 2015 17:31:51 +0000 (19:31 +0200)]
bug fix in extconf
Adam Sieradzan [Tue, 22 Sep 2015 08:10:57 +0000 (10:10 +0200)]
working shielding
Adam Sieradzan [Wed, 9 Sep 2015 11:15:16 +0000 (13:15 +0200)]
changes in parameter file and debug off
Adam Sieradzan [Wed, 9 Sep 2015 10:23:28 +0000 (12:23 +0200)]
new lipid potentials
Adam Sieradzan [Tue, 8 Sep 2015 09:13:17 +0000 (11:13 +0200)]
Shielding part 2
Adam Sieradzan [Tue, 1 Sep 2015 14:29:59 +0000 (16:29 +0200)]
introduction of shielding effect (volume of overlap)
Adam Sieradzan [Thu, 6 Aug 2015 08:39:41 +0000 (10:39 +0200)]
Merge branch 'devel' into AFM
Conflicts:
.gitignore
PARAM/pot_theta_G631_DIL.parm
bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe
bin/unres/MD/unres_Tc_procor_oldparm_em64-D-symetr.exe
bin/unres/MD/unres_ifort_MPICH_GAB.exe
bin/xdrf2ang
bin/xdrf2pdb
bin/xdrf2pdb-m
source/cluster/wham/src-M/energy_p_new.F
source/maxlik/src_CSA/CMakeLists.txt
source/unres/src_CSA_DiL/CMakeLists.txt
source/unres/src_CSA_DiL/Makefile
source/unres/src_CSA_DiL/csa.F
source/unres/src_MD-M/COMMON.CONTROL
source/unres/src_MD-M/DIMENSIONS
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/cinfo.f
source/unres/src_MD-M/energy_p_new_barrier.F
source/unres/src_MD-M/parmread.F
source/unres/src_MD-M/refsys.f
source/unres/src_MD/COMMON.TORSION
source/wham/src-M/DIMENSIONS
source/wham/src-M/energy_p_new.F
source/wham/src-M/readrtns.F
source/xdrfpdb/src/Makefile
Adam Sieradzan [Thu, 6 Aug 2015 08:13:44 +0000 (10:13 +0200)]
first changes for shielding
Adam Sieradzan [Thu, 6 Aug 2015 07:01:16 +0000 (09:01 +0200)]
Merge branch 'AFM' into multichain
Adam Sieradzan [Thu, 6 Aug 2015 06:59:38 +0000 (08:59 +0200)]
intoduction of constant velocity for spring
Adam Sieradzan [Mon, 3 Aug 2015 19:41:28 +0000 (21:41 +0200)]
adding of sccor am1 parameter file
Adam Sieradzan [Mon, 3 Aug 2015 19:39:58 +0000 (21:39 +0200)]
1) debug of Lorentzian like constrains in cluster 2) introduction of constrains on theta angle
Adam Sieradzan [Sun, 2 Aug 2015 19:11:46 +0000 (21:11 +0200)]
first introduction of valence constrains - not working yet
Adam Sieradzan [Fri, 31 Jul 2015 10:24:38 +0000 (12:24 +0200)]
introduction of different ftors for each site
Adam Sieradzan [Fri, 31 Jul 2015 07:36:14 +0000 (09:36 +0200)]
First trial to introduce steered MD non successful
Adam Sieradzan [Tue, 28 Jul 2015 10:21:39 +0000 (12:21 +0200)]
Intoduction Lorentizan like restrains to cluster
Adam Sieradzan [Tue, 21 Jul 2015 05:57:41 +0000 (07:57 +0200)]
WHAM for Lorentzian like constrains fixed - DEBUG OFF
Adam Sieradzan [Mon, 20 Jul 2015 08:39:38 +0000 (10:39 +0200)]
debuging WHAM for constrains DEBUG ON
Adam Sieradzan [Fri, 17 Jul 2015 12:11:56 +0000 (14:11 +0200)]
first attempt to indroduce AFM velocity
Adam Sieradzan [Fri, 10 Jul 2015 11:46:08 +0000 (13:46 +0200)]
introduction of quartic an Lonrentz constrains to WHAM
Adam Sieradzan [Mon, 6 Jul 2015 09:21:26 +0000 (11:21 +0200)]
Merge branch 'multichain' of mmka:unres into multichain
Adam Sieradzan [Mon, 6 Jul 2015 09:17:47 +0000 (11:17 +0200)]
intoduction of quartic restrains in multichain, bugfix in single chain
Adam Sieradzan [Fri, 3 Jul 2015 11:16:13 +0000 (13:16 +0200)]
WeFold Lorentzian like potentials introduction
rojas [Tue, 30 Jun 2015 14:49:35 +0000 (10:49 -0400)]
Change in energy_p_new_barrier.F, in eelec, aorund line 3065
Because in general iturn3_start and iturn3_end are nnt and nct-3,
respectively, if the chain has a GLY as the first or last residues,
nnt=1 or nct=nres, the program ends up evaluating itype(0) or itype(nres+1).
The first case causes a segmentation fault, the second won't (if maxres is
bigger than nres), but it won't cycle the loop which is what was intended
Adam Sieradzan [Fri, 26 Jun 2015 18:44:39 +0000 (20:44 +0200)]
Changes suggested by Ana
Adam Sieradzan [Thu, 25 Jun 2015 10:36:18 +0000 (12:36 +0200)]
Merge branch 'lipid' into AFM
Adam Sieradzan [Thu, 25 Jun 2015 10:34:42 +0000 (12:34 +0200)]
removal of double returnbox
Adam Sieradzan [Thu, 25 Jun 2015 10:31:05 +0000 (12:31 +0200)]
Merge branch 'multichain' into lipid
Conflicts:
source/unres/src_MD-M/MREMD.F
Dawid Jagiela [Wed, 24 Jun 2015 10:00:29 +0000 (12:00 +0200)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Dawid Jagiela [Wed, 24 Jun 2015 09:59:40 +0000 (11:59 +0200)]
removed uninitialized ghalf from equation
Adam Sieradzan [Tue, 23 Jun 2015 09:07:31 +0000 (11:07 +0200)]
small fix in lipids
Adam Sieradzan [Wed, 27 May 2015 04:27:06 +0000 (06:27 +0200)]
working cluster for dyn_ss and triss
Adam Sieradzan [Tue, 26 May 2015 13:01:14 +0000 (15:01 +0200)]
Debug cluster part 2
Adam Sieradzan [Tue, 26 May 2015 12:40:36 +0000 (14:40 +0200)]
Cluster debug ON
Adam Sieradzan [Tue, 26 May 2015 12:27:22 +0000 (14:27 +0200)]
havebond turnoff
Adam Sieradzan [Tue, 26 May 2015 12:10:27 +0000 (14:10 +0200)]
correction of readrtns
Adam Sieradzan [Tue, 26 May 2015 11:44:09 +0000 (13:44 +0200)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Tue, 26 May 2015 11:43:17 +0000 (13:43 +0200)]
energy_dec to logical
Dawid Jagiela [Tue, 26 May 2015 02:35:42 +0000 (04:35 +0200)]
removed obsolite code in ssMD.F files
Adam Sieradzan [Tue, 26 May 2015 01:16:29 +0000 (03:16 +0200)]
Introduction of dyn_ss and triss to cluster
Adam Sieradzan [Mon, 25 May 2015 12:20:55 +0000 (14:20 +0200)]
hidden part of debug
Adam Sieradzan [Mon, 25 May 2015 11:25:59 +0000 (13:25 +0200)]
nss*ebr removed
Adam Sieradzan [Mon, 25 May 2015 11:07:23 +0000 (13:07 +0200)]
cxread debug 7
Adam Sieradzan [Mon, 25 May 2015 10:43:12 +0000 (12:43 +0200)]
debug part 6
Adam Sieradzan [Mon, 25 May 2015 10:35:17 +0000 (12:35 +0200)]
Debug 5
Adam Sieradzan [Mon, 25 May 2015 10:26:13 +0000 (12:26 +0200)]
another DEBUG
Adam Sieradzan [Mon, 25 May 2015 10:12:24 +0000 (12:12 +0200)]
dubug dss part 3
Adam Sieradzan [Mon, 25 May 2015 09:53:19 +0000 (11:53 +0200)]
diffrent name for evdw
Adam Sieradzan [Mon, 25 May 2015 09:42:36 +0000 (11:42 +0200)]
TRISS debug
Adam Sieradzan [Mon, 25 May 2015 09:27:00 +0000 (11:27 +0200)]
Warnig Debug ON
Adam Sieradzan [Sun, 24 May 2015 12:46:48 +0000 (14:46 +0200)]
Corrected WHAM and UNRES reading in SS dyn...
Adam Sieradzan [Sat, 23 May 2015 10:52:08 +0000 (12:52 +0200)]
Introduction of working dyn_ss and triss. Problems were due to different input format style
Adam Sieradzan [Sat, 23 May 2015 10:00:56 +0000 (12:00 +0200)]
Correction in readrtns
Adam Sieradzan [Sat, 23 May 2015 09:56:20 +0000 (11:56 +0200)]
Change in line of dyn_ss
Adam Sieradzan [Fri, 22 May 2015 21:25:20 +0000 (23:25 +0200)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Fri, 22 May 2015 21:24:45 +0000 (23:24 +0200)]
Adding dyn_ss and triss potentials to src-M wham
Pawel Krupa [Fri, 22 May 2015 12:36:39 +0000 (14:36 +0200)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Pawel Krupa [Fri, 22 May 2015 12:33:20 +0000 (14:33 +0200)]
Fixed bug in reading trisulfide potentials (atriss, btriss, ctriss, dtriss).
Dawid Jagiela [Wed, 6 May 2015 18:56:05 +0000 (20:56 +0200)]
fixed install binary paths
Adam Sieradzan [Wed, 6 May 2015 10:33:08 +0000 (12:33 +0200)]
correction in readpdb (bugfix)
Adam Sieradzan [Thu, 23 Apr 2015 09:31:02 +0000 (11:31 +0200)]
zmiany w geomout dla AFM
Pawel Krupa [Tue, 21 Apr 2015 23:18:13 +0000 (01:18 +0200)]
MPICH2 and energy fixes in WHAM-M and Cluster-M.
Adam Sieradzan [Fri, 17 Apr 2015 19:35:05 +0000 (21:35 +0200)]
Merge branch 'devel' of mmka:unres into devel
Pawel Krupa [Fri, 17 Apr 2015 19:29:59 +0000 (21:29 +0200)]
Fixed error caused by new MPICH2, which made WHAM-M non-usable.
Adam Sieradzan [Fri, 17 Apr 2015 17:50:27 +0000 (19:50 +0200)]
poprawka w COMMON.SBRIDE dla triss
Adam Sieradzan [Fri, 17 Apr 2015 17:44:02 +0000 (19:44 +0200)]
Zaimplementowany AFM
Pawel Krupa [Thu, 16 Apr 2015 20:58:27 +0000 (22:58 +0200)]
Fixed energy differs in WHAM-M (EBE).
Adam Sieradzan [Mon, 13 Apr 2015 15:12:45 +0000 (17:12 +0200)]
poprawka w intcartderiv
Adam Sieradzan [Mon, 13 Apr 2015 15:07:52 +0000 (17:07 +0200)]
Introduction of SS to newcorr and SSS to src_MD-M
Adam Sieradzan [Thu, 9 Apr 2015 07:56:22 +0000 (09:56 +0200)]
poprawka w pametrach
Dawid Jagiela [Sun, 5 Apr 2015 21:04:43 +0000 (23:04 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Sun, 5 Apr 2015 20:29:31 +0000 (22:29 +0200)]
added Force-Fields descriptions in exe filenames
Pawel Krupa [Thu, 26 Mar 2015 19:05:59 +0000 (20:05 +0100)]
MD problems fixed with FGPROC>1
Adam Sieradzan [Wed, 25 Mar 2015 08:51:15 +0000 (09:51 +0100)]
important change for single processor for multi-chain
Adam Sieradzan [Thu, 19 Mar 2015 09:43:55 +0000 (10:43 +0100)]
chyba dzialajacy lipid
Adam Sieradzan [Wed, 18 Mar 2015 13:11:32 +0000 (14:11 +0100)]
Merge branch 'multichain' into lipid
Conflicts:
source/unres/src_MD-M/energy_p_new_barrier.F
source/unres/src_MD-M/unres.F
Adam Sieradzan [Wed, 18 Mar 2015 13:08:28 +0000 (14:08 +0100)]
correction of correlation potentials
Adam Sieradzan [Wed, 18 Mar 2015 12:45:34 +0000 (13:45 +0100)]
poprawki w potencjalach
Adam Sieradzan [Mon, 16 Mar 2015 09:59:30 +0000 (10:59 +0100)]
drobne poprawki
Adam Sieradzan [Wed, 4 Mar 2015 21:12:29 +0000 (22:12 +0100)]
Merge branch 'multichain' of mmka:unres into lipid
Adam Sieradzan [Wed, 4 Mar 2015 21:05:57 +0000 (22:05 +0100)]
correction in multichain
Adam Sieradzan [Wed, 4 Mar 2015 20:10:38 +0000 (21:10 +0100)]
introduce lipid good grad wrong symplex
Adam Sieradzan [Tue, 24 Feb 2015 11:10:50 +0000 (12:10 +0100)]
Merge branch 'master' into multichain
Conflicts:
.gitignore
source/unres/src_MD-M/energy_p_new_barrier.F
Adam Sieradzan [Thu, 19 Feb 2015 11:43:23 +0000 (12:43 +0100)]
poprawki w ANG w src_MD-M
Adam Sieradzan [Tue, 10 Feb 2015 11:54:18 +0000 (12:54 +0100)]
wprowadzenie lipidow
Adam Liwo [Fri, 23 Jan 2015 20:29:12 +0000 (21:29 +0100)]
Corrected refsys.f in src_MD-M
Conflicts:
bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/cinfo.f
source/unres/src_MD-M/readpdb.F
Adam Sieradzan [Thu, 29 Jan 2015 07:46:52 +0000 (08:46 +0100)]
Introduction of lipid energy transfer
Adam Sieradzan [Wed, 17 Dec 2014 09:48:55 +0000 (10:48 +0100)]
Merge branch 'master' of mmka:unres
Conflicts:
.gitignore
bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
bin/unres/MD/unres_gfortran_single_GAB.exe
bin/unres/MD/unres_ifort_single_GAB.exe
bin/unres/MINIM/unres_ifort_MIN_single_E0LL2Y.exe
bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe
bin/unres_clustMD_MPI-oldparm
bin/wham/wham_multparm-ham_rep-oldparm
source/cluster/wham/src/COMMON.SCCOR
source/cluster/wham/src/Makefile
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/energy_p_new_barrier.F
source/unres/src_MD-M/stochfric.F
source/unres/src_MD/cinfo.f
source/wham/src-M/Makefile
source/wham/src/DIMENSIONS.FREE
Adam Sieradzan [Wed, 17 Dec 2014 09:42:35 +0000 (10:42 +0100)]
zmiany w gitignore
Adam Sieradzan [Wed, 17 Dec 2014 09:40:58 +0000 (10:40 +0100)]
Merge branch 'master' of mmka:unres into multichain
Conflicts:
.gitignore
bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
bin/unres/MD/unres_gfortran_single_GAB.exe
bin/unres/MD/unres_ifort_single_GAB.exe
bin/unres/MINIM/unres_ifort_MIN_single_E0LL2Y.exe
bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe
bin/unres_clustMD_MPI-oldparm
bin/wham/wham_multparm-ham_rep-oldparm
source/cluster/wham/src/COMMON.SCCOR
source/cluster/wham/src/Makefile
source/unres/src_MD-M/MREMD.F
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/energy_p_new_barrier.F
source/unres/src_MD-M/stochfric.F
source/unres/src_MD-M/unres.F
source/unres/src_MD/cinfo.f
source/wham/src-M/Makefile
source/wham/src/DIMENSIONS.FREE
Adam Liwo [Thu, 11 Dec 2014 14:37:42 +0000 (15:37 +0100)]
Minor change in documentation (installman)
Adam Liwo [Thu, 11 Dec 2014 14:36:04 +0000 (15:36 +0100)]
Updated changelog, added minimization-only version binaries
Adam Liwo [Thu, 11 Dec 2014 14:14:41 +0000 (15:14 +0100)]
Created binaries and fixed bugs when compiling single-processor version of the multichain code.
Dawid Jagieła [Sun, 7 Dec 2014 15:30:55 +0000 (16:30 +0100)]
removed CSA_DiL sources from CMake