Adam Liwo [Sat, 1 Aug 2015 08:52:06 +0000 (10:52 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Cezary Czaplewski [Sat, 1 Aug 2015 08:40:37 +0000 (10:40 +0200)]
read2sigma - now without this option code works as before
Adam Liwo [Fri, 31 Jul 2015 23:02:13 +0000 (01:02 +0200)]
pulled readrtns
Cezary Czaplewski [Fri, 31 Jul 2015 19:33:28 +0000 (21:33 +0200)]
restoring read2sigma code after wrong merge
Cezary Czaplewski [Fri, 31 Jul 2015 14:52:00 +0000 (16:52 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
source/unres/src_MD/readrtns.F
resolved
Cezary Czaplewski [Fri, 31 Jul 2015 14:23:15 +0000 (16:23 +0200)]
new format of read2sigma *sco files (res number in 1st column)
and correction for Gly as 1st residue
Adam Liwo [Fri, 31 Jul 2015 14:15:37 +0000 (16:15 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
source/unres/src_MD/readrtns.F
Adam Liwo [Fri, 31 Jul 2015 14:06:13 +0000 (16:06 +0200)]
By AL: fixed FGPROCS>1 problem in HMREMD; iset passed to slaves now.
Minor modification in molread: prints the names of the pdb files with the modesls.
Cezary Czaplewski [Tue, 28 Jul 2015 08:38:19 +0000 (10:38 +0200)]
bugfix for read2sigma with different domain definition in each *sco file
necessary for finegrain parallelization
Cezary Czaplewski [Tue, 21 Jul 2015 13:39:09 +0000 (15:39 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Cezary Czaplewski [Tue, 21 Jul 2015 13:37:27 +0000 (15:37 +0200)]
read2sigma supports separate domain definition in each *sco file
Adam Liwo [Sat, 18 Jul 2015 11:28:14 +0000 (13:28 +0200)]
Added putting secondary-structure information to the pdbfiles generated by xdrf2pdb. Enabled by compling xdrf2pdb with -DSECONDARY
Adam Liwo [Fri, 17 Jul 2015 23:09:08 +0000 (01:09 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Adam Liwo [Fri, 17 Jul 2015 23:08:28 +0000 (01:08 +0200)]
Added Makefiles
Cezary Czaplewski [Fri, 17 Jul 2015 10:48:27 +0000 (12:48 +0200)]
the first version of READ2SIGMA - the same domains in all *sco files,
readpdb_template cannot read pdb files with gaps
Adam Liwo [Thu, 9 Jul 2015 18:40:46 +0000 (20:40 +0200)]
Fixed the "***" issue in PDB output format by shifting the center of each molecule to 0
Adam Liwo [Sun, 28 Jun 2015 19:27:45 +0000 (21:27 +0200)]
Fixes to compile WHAM and CLUSTER on AIX (nostromo.icm.edu.pl)
Adam Liwo [Wed, 17 Jun 2015 12:59:54 +0000 (14:59 +0200)]
Added ifdefs to include/exlucde DFA becuase of the large memory requirement problem with DFA.
Adam Liwo [Fri, 12 Jun 2015 14:23:42 +0000 (16:23 +0200)]
Fixed the homology gradient in finegrain mode
Adam Liwo [Sun, 7 Jun 2015 07:18:16 +0000 (09:18 +0200)]
Added an option to compile unres, wham, and cluster on the homology branch
with old (incorrect) weights; the comiple flag is -DOLDSIGMA
Adam Liwo [Sun, 7 Jun 2015 06:43:31 +0000 (08:43 +0200)]
Fixes made in connection to Hamiltonian replica exchange in homology restraints
1. WHAM - in wham_calc; restraints windows were not incuded in the iteration
process and in calculation of thermal characteristics.
2. Cluster - restraints were not included properly in calculating probabilities
of conformations; now the user inputs all restraint weights and
selects the weight with which to do clustering by saying ISET=??? on the
homology_nset card
Imported the fix of the distance-restraint-weight calculations that Felipe made
as a result of the June 3 project meeting (Felipe had problems pushing his
changes).
Adam Liwo [Thu, 28 May 2015 05:07:13 +0000 (07:07 +0200)]
Fixed main module of WHAM
Adam Liwo [Thu, 14 May 2015 09:34:07 +0000 (11:34 +0200)]
Fixed the following components:
- wham: in whamcalc1.F added ehomology_constr and DFA energy components to
the minimal free energies; lack of this was often causing NaNs in
the *.thermal files.
- cluster: (i) assigned logical unit 38 to ientin (unasigned in the previou
source; (ii) Fixed buffer conflict in MPI_AllGather
- wham and cluster: ebend made compatible with that of the unres component
Adam Liwo [Wed, 13 May 2015 13:16:45 +0000 (15:16 +0200)]
Fixed a MAJOR error in WHAM; energies were computed inconsistently
Cezary Czaplewski [Thu, 7 May 2015 08:53:22 +0000 (10:53 +0200)]
cmake compilation for cluster and wham repaired
Cezary Czaplewski [Wed, 6 May 2015 10:58:40 +0000 (12:58 +0200)]
minimization in int works with FGPROCS>1
(+some cleaning of debug print and MPICH2 as default in Makefile)
Felipe Pineda [Thu, 16 Apr 2015 07:56:39 +0000 (09:56 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
source/unres/src_MD/cinfo.f
Felipe Pineda [Thu, 16 Apr 2015 07:46:48 +0000 (09:46 +0200)]
WHAM and CLUSTER with HM restraints by AL and FP
Cezary Czaplewski [Tue, 17 Mar 2015 16:04:38 +0000 (17:04 +0100)]
remd with homol_nset>1 working with FG parallelization
Cezary Czaplewski [Fri, 13 Mar 2015 13:38:56 +0000 (14:38 +0100)]
changes to avoid PMPI_Scatterv: Invalid buffer pointer in Intel MPI
Felipe Pineda [Fri, 6 Mar 2015 10:53:41 +0000 (11:53 +0100)]
Lorentzian-type distance restraint energy implemented
Felipe Pineda [Wed, 4 Mar 2015 10:28:55 +0000 (11:28 +0100)]
common.control cleaning
Felipe Pineda [Wed, 4 Mar 2015 10:22:26 +0000 (11:22 +0100)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
source/unres/src_MD/COMMON.CONTROL
source/unres/src_MD/cinfo.f
Felipe Pineda [Wed, 4 Mar 2015 10:18:07 +0000 (11:18 +0100)]
After final fix by AL
Cezary Czaplewski [Tue, 3 Mar 2015 11:55:08 +0000 (12:55 +0100)]
REMD with HOMOL_NSET>1 and single weight for all homology restraints
some output cleaning
Felipe Pineda [Wed, 25 Feb 2015 14:03:08 +0000 (15:03 +0100)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
bin/unres/MD/unres_ifort_MPICH_E0LL2Y_2.exe
source/unres/src_MD/cinfo.f
Felipe Pineda [Wed, 25 Feb 2015 11:41:44 +0000 (12:41 +0100)]
Merge branch 'master' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
bin/unres/MD/unres_ifort_MPICH_GAB.exe
source/unres/src_MD/MREMD.F
source/unres/src_MD/cinfo.f
Cezary Czaplewski [Wed, 25 Feb 2015 09:55:25 +0000 (10:55 +0100)]
respa now working without dfa weights
Felipe Pineda [Fri, 20 Feb 2015 10:23:07 +0000 (11:23 +0100)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Conflicts:
bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
source/unres/src_MD/COMMON.CONTROL
source/unres/src_MD/cinfo.f
source/unres/src_MD/energy_p_new_barrier.F
source/unres/src_MD/readrtns.F
Cezary Czaplewski [Fri, 20 Feb 2015 09:07:29 +0000 (10:07 +0100)]
Merge branch 'prerelease-3.2.1'
Adam Sieradzan [Thu, 19 Feb 2015 17:41:51 +0000 (18:41 +0100)]
EBE change in prerealese-3.2.1 make dummy atom idependent
Adam Sieradzan [Mon, 16 Feb 2015 12:36:45 +0000 (13:36 +0100)]
poprawka w src_MD
Adam Sieradzan [Mon, 16 Feb 2015 12:34:30 +0000 (13:34 +0100)]
Poprawiony src_MD-M gradient
Felipe Pineda [Thu, 12 Feb 2015 13:54:55 +0000 (14:54 +0100)]
1st running version of UNRES HM by FP and AL
Adam Sieradzan [Wed, 11 Feb 2015 16:06:45 +0000 (17:06 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Adam Sieradzan [Wed, 11 Feb 2015 16:05:21 +0000 (17:05 +0100)]
rozgrzebana minimalizacja
Adam Sieradzan [Wed, 11 Feb 2015 11:23:12 +0000 (12:23 +0100)]
intro of SCCOR into src_MIN
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/cinfo.f
Dawid Jagieła [Sat, 24 Jan 2015 22:10:14 +0000 (23:10 +0100)]
removed maxlik paths from cmake sources
Adam Liwo [Fri, 23 Jan 2015 20:34:54 +0000 (21:34 +0100)]
refsys
Adam Liwo [Fri, 23 Jan 2015 20:30:52 +0000 (21:30 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Conflicts:
source/unres/src_MD-M/cinfo.f
source/unres/src_MD-M/refsys.f
Adam Liwo [Fri, 23 Jan 2015 20:29:12 +0000 (21:29 +0100)]
Corrected refsys.f in src_MD-M
Adam Sieradzan [Thu, 22 Jan 2015 10:18:23 +0000 (11:18 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Adam Sieradzan [Mon, 19 Jan 2015 13:32:01 +0000 (14:32 +0100)]
dzialajacy wham+poprawka w funckji energi+ poprawka w czytaniu
Cezary Czaplewski [Thu, 8 Jan 2015 08:01:20 +0000 (09:01 +0100)]
dfa.F was missing form cmake configurations files
Cezary Czaplewski [Thu, 8 Jan 2015 07:49:23 +0000 (08:49 +0100)]
Makefiles for mpich2 and some corrections to Makefiles
Adam Liwo [Mon, 5 Jan 2015 05:50:09 +0000 (06:50 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Conflicts:
source/unres/src_MD-M/cinfo.f
source/wham/src-M/cinfo.f
Adam Liwo [Mon, 5 Jan 2015 05:46:39 +0000 (06:46 +0100)]
Added cinfo
Adam Liwo [Mon, 5 Jan 2015 05:43:41 +0000 (06:43 +0100)]
MREMD corrected; Langevin mode (bcast instead of scatter i2rep)
Adam Sieradzan [Sun, 4 Jan 2015 11:33:52 +0000 (12:33 +0100)]
poprawka gradientu w CSA
Adam Sieradzan [Sun, 4 Jan 2015 10:54:16 +0000 (11:54 +0100)]
Naprawienie wham'a oraz wprowadzenie SCcorr do CSA
Adam Sieradzan [Tue, 30 Dec 2014 11:04:30 +0000 (12:04 +0100)]
wprowadzenie do multichaina SCcorr
Adam Sieradzan [Fri, 19 Dec 2014 12:29:56 +0000 (13:29 +0100)]
debug w poszukiwaniu bledu w ostatniej reszcie
Adam Kazimierz Sieradzan [Tue, 30 Oct 2012 11:33:45 +0000 (07:33 -0400)]
dodanie czytania wagi wsccor do clustrowania-M
Conflicts:
bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
source/cluster/wham/src-M/readrtns.o
Adam Kazimierz Sieradzan [Tue, 30 Oct 2012 11:16:58 +0000 (07:16 -0400)]
Wstawnieni SCCOR dla clustrowania. Nie wiadomo czy jest czytana waga
Conflicts:
bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
bin/wham_multparm-D-sccor-oldparm
source/cluster/wham/src-M/COMMON.SCCOR
source/cluster/wham/src-M/chainbuild.o
source/cluster/wham/src-M/convert.o
source/cluster/wham/src-M/energy_p_new.F
source/cluster/wham/src-M/energy_p_new.o
source/cluster/wham/src-M/geomout.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/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/setup_var.o
source/cluster/wham/src-M/wrtclust.o
source/cluster/wham/src-M/xdrf/libxdrf.a
Adam Kazimierz Sieradzan [Mon, 29 Oct 2012 12:37:44 +0000 (08:37 -0400)]
Wprowadzenie SCCOR dla wham-M
Conflicts:
bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
bin/wham_multparm-D-sccor-oldparm
source/unres/src_MD-M/cinfo.f
source/wham/src-M/COMMON.ALLPARM
source/wham/src-M/cinfo.f
source/wham/src-M/energy_p_new.F
source/wham/src-M/include_unres/COMMON.LOCAL
source/wham/src-M/include_unres/COMMON.SCCOR
source/wham/src/include_unres/COMMON.SCCOR
Adam Kazimierz Sieradzan [Fri, 26 Oct 2012 09:47:18 +0000 (05:47 -0400)]
Rozgrzebany SCCOR dla wham-M
Conflicts:
source/wham/src-M/energy_p_new.F
Adam Kazimierz Sieradzan [Fri, 5 Oct 2012 11:17:17 +0000 (07:17 -0400)]
Poprawiony SCR_MD-M i dzialajacy
Conflicts:
source/unres/src_MD-M/initialize_p.F
source/unres/src_MD-M/parmread.F
Adam Kazimierz Sieradzan [Thu, 4 Oct 2012 14:52:15 +0000 (10:52 -0400)]
Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
D aminokwasow
Conflicts:
bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
source/unres/src_MD-M/COMMON.SCCOR
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/lagrangian_lesyng.F
source/unres/src_MD-M/moments.f
source/unres/src_MD-M/parmread.F
source/unres/src_MD-M/stochfric.F
source/unres/src_MD/COMMON.SCCOR
Adam Sieradzan [Wed, 17 Dec 2014 10:06:19 +0000 (11:06 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagiela [Fri, 12 Dec 2014 14:15:37 +0000 (15:15 +0100)]
removed source/maxlik/src_CSA dir from CMake
Adam Liwo [Fri, 12 Dec 2014 00:48:20 +0000 (01:48 +0100)]
Again, documentation updated
Adam Liwo [Fri, 12 Dec 2014 00:43:11 +0000 (01:43 +0100)]
Documentation updated
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
Cezary Czaplewski [Fri, 5 Dec 2014 13:32:31 +0000 (14:32 +0100)]
correction to 4P energy and csa examples
Cezary Czaplewski [Fri, 5 Dec 2014 13:16:25 +0000 (14:16 +0100)]
corrected example CSA run with 4P
Cezary Czaplewski [Fri, 5 Dec 2014 12:44:53 +0000 (13:44 +0100)]
new options for mpich2 with gfortran Makefile
Cezary Czaplewski [Fri, 5 Dec 2014 10:39:17 +0000 (11:39 +0100)]
src_CSA_DiL removed from prerelease, current version in devel
Adam Liwo [Thu, 4 Dec 2014 13:54:48 +0000 (14:54 +0100)]
Added the change docs by Adam
Adam Liwo [Thu, 4 Dec 2014 13:52:45 +0000 (14:52 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Adam Liwo [Thu, 4 Dec 2014 13:51:12 +0000 (14:51 +0100)]
Yet more changes in the documentation ( by Adam)
Adam Liwo [Thu, 4 Dec 2014 13:40:17 +0000 (14:40 +0100)]
Revised documentation by Adam
Cezary Czaplewski [Fri, 28 Nov 2014 13:44:28 +0000 (14:44 +0100)]
testing 2D replica exchange with FPROCS>1
Dawid Jagiela [Fri, 28 Nov 2014 12:37:21 +0000 (13:37 +0100)]
changed FF preprocesor flags in src_CSA_DiL/CMakeLists.txt
Dawid Jagiela [Fri, 28 Nov 2014 11:49:03 +0000 (12:49 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Adam Liwo [Fri, 28 Nov 2014 11:42:27 +0000 (12:42 +0100)]
Updated INSTALL
Adam Liwo [Fri, 28 Nov 2014 11:38:33 +0000 (12:38 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Dawid Jagiela [Fri, 28 Nov 2014 11:38:22 +0000 (12:38 +0100)]
fixed FF preprocesor flags for src_CSA/CMakeLists.txt
Adam Liwo [Fri, 28 Nov 2014 11:37:12 +0000 (12:37 +0100)]
Updated INSTALL
By Adam
Dawid Jagiela [Fri, 28 Nov 2014 11:24:28 +0000 (12:24 +0100)]
changed csa.f to csa.F in src_CSA/CMakeLists.txt sources
Adam Liwo [Fri, 28 Nov 2014 10:45:13 +0000 (11:45 +0100)]
Trying to bring files - continued
By Adam
Adam Liwo [Fri, 28 Nov 2014 10:37:50 +0000 (11:37 +0100)]
Trying to bring the csa.F file to the repository.
By Adam.
Adam Liwo [Thu, 27 Nov 2014 14:53:46 +0000 (15:53 +0100)]
Additional fix of xdrfpdb binaries (creation of bin/xdrf and putting
binaries there acc. to documentation.
By Adam
Adam Liwo [Thu, 27 Nov 2014 14:35:35 +0000 (15:35 +0100)]
Fixed Makefiles, handle all force fields thru appropriate options
By Adam
Cezary Czaplewski [Sun, 9 Nov 2014 14:58:07 +0000 (15:58 +0100)]
restart is now working with HOMOL_NSET
Cezary Czaplewski [Fri, 7 Nov 2014 23:06:47 +0000 (00:06 +0100)]
untrack *.exe in git
Cezary Czaplewski [Fri, 7 Nov 2014 13:54:15 +0000 (14:54 +0100)]
some corrections to 2D replica exchange with homology
projects / unres.git / log