Cezary Czaplewski [Sat, 14 Mar 2020 14:13:58 +0000 (15:13 +0100)]
rm exe
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 [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 [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 [Fri, 31 Jul 2015 07:36:14 +0000 (09:36 +0200)]
First trial to introduce steered MD non successful
Adam Sieradzan [Fri, 17 Jul 2015 12:11:56 +0000 (14:11 +0200)]
first attempt to indroduce AFM velocity
Adam Sieradzan [Mon, 6 Jul 2015 09:21:26 +0000 (11:21 +0200)]
Merge branch 'multichain' of mmka:unres into multichain
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
Adam Sieradzan [Tue, 23 Jun 2015 09:07:31 +0000 (11:07 +0200)]
small fix in lipids
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
Adam Sieradzan [Fri, 17 Apr 2015 17:44:02 +0000 (19:44 +0200)]
Zaimplementowany AFM
Adam Sieradzan [Thu, 9 Apr 2015 07:56:22 +0000 (09:56 +0200)]
poprawka w pametrach
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 [Tue, 10 Feb 2015 11:54:18 +0000 (12:54 +0100)]
wprowadzenie lipidow
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
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
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
Dawid Jagiela [Wed, 5 Nov 2014 21:44:43 +0000 (22:44 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagiela [Wed, 5 Nov 2014 21:44:05 +0000 (22:44 +0100)]
ctest ala10 binary location fix
Dawid Jagieła [Wed, 5 Nov 2014 08:56:10 +0000 (09:56 +0100)]
Added CMake build instructions
Dawid Jagiela [Fri, 31 Oct 2014 22:48:33 +0000 (23:48 +0100)]
fix for multiple MPI include paths passed by MPI wrapper
Dawid Jagiela [Mon, 27 Oct 2014 22:19:36 +0000 (23:19 +0100)]
1) binaries are compiled into /bin subdirectory of build directory
2) added "make install" support costumizable with CMAKE_INSTALL_PREFIX
Dawid Jagiela [Sun, 26 Oct 2014 21:58:46 +0000 (22:58 +0100)]
1) Threading cleanup in src_CSA & src_CSA_DiL
2) Makefile verbose turned off for "Release" builds
3) fixed missing printmat.f in cluster/wham/src/CMakeLists.txt
Dawid Jagiela [Sun, 26 Oct 2014 16:03:50 +0000 (17:03 +0100)]
switched to CMake FindMPI module in all source files that use MPI
Dawid Jagiela [Sun, 26 Oct 2014 14:33:10 +0000 (15:33 +0100)]
added missing preprocessor flags for prng_32.F
Dawid Jagiela [Sat, 25 Oct 2014 21:45:17 +0000 (23:45 +0200)]
prng.f unification
Adam Sieradzan [Thu, 23 Oct 2014 15:56:55 +0000 (17:56 +0200)]
Merge branch 'multichain' of mmka:unres into multichain
Adam Sieradzan [Thu, 23 Oct 2014 15:56:27 +0000 (17:56 +0200)]
poprawka w stochasticfric
Dawid Jagiela [Thu, 16 Oct 2014 23:51:51 +0000 (01:51 +0200)]
64-bit fix for unres/CSA and unres/CSA_DiL code
Dawid Jagieła [Tue, 14 Oct 2014 22:30:49 +0000 (00:30 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagieła [Tue, 14 Oct 2014 22:29:43 +0000 (00:29 +0200)]
fixed CMake variable typo
Cezary Czaplewski [Wed, 8 Oct 2014 10:32:04 +0000 (12:32 +0200)]
correct default option for compilers in cluster CmakeList.txt
Cezary Czaplewski [Wed, 8 Oct 2014 10:09:44 +0000 (12:09 +0200)]
correct default option for compilers in wham CmakeList.txt
Adam Kazimierz Sieradzan [Thu, 11 Sep 2014 19:14:53 +0000 (15:14 -0400)]
poprawka w triss
Adam Sieradzan [Wed, 10 Sep 2014 14:23:12 +0000 (16:23 +0200)]
correction of xdrf2pdb
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
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
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).
projects / unres.git / log