unres.git
12 years agoWprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
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

12 years agozmiany 20 na typ w src_md-M
Adam Kazimierz Sieradzan [Tue, 2 Oct 2012 07:20:47 +0000 (03:20 -0400)]
zmiany 20 na typ w src_md-M

12 years agoZMiana w parmreadzie
Adam Kazimierz Sieradzan [Tue, 2 Oct 2012 06:57:48 +0000 (02:57 -0400)]
ZMiana w parmreadzie

12 years agopoprawka w src-MD
Adam Kazimierz Sieradzan [Thu, 6 Sep 2012 10:45:27 +0000 (06:45 -0400)]
poprawka w src-MD

12 years agoUNRES caly zmienione 21 na ntyp1
Adam Kazimierz Sieradzan [Fri, 31 Aug 2012 16:46:12 +0000 (12:46 -0400)]
UNRES caly zmienione 21 na ntyp1

12 years agoZmina 21 na ntyp1 w wham src i src-M
Adam Kazimierz Sieradzan [Fri, 31 Aug 2012 14:51:26 +0000 (10:51 -0400)]
Zmina 21 na ntyp1 w wham src i src-M

12 years agoZmiana 21 na ntyp1 w unres SRC_MD oraz SRC_MD-M
Adam Kazimierz Sieradzan [Fri, 31 Aug 2012 08:40:36 +0000 (04:40 -0400)]
Zmiana 21 na ntyp1 w unres SRC_MD oraz SRC_MD-M

12 years agoDzialajacy cluster dla D aminokwasow
Adam Kazimierz Sieradzan [Wed, 29 Aug 2012 11:41:32 +0000 (07:41 -0400)]
Dzialajacy cluster dla D aminokwasow

12 years agoZmiany do clustrowania dla D aminokwasow single chain.
Adam Kazimierz Sieradzan [Tue, 28 Aug 2012 13:33:32 +0000 (09:33 -0400)]
Zmiany do clustrowania dla D aminokwasow single chain.

12 years agoDzialajaczy dla D aminokwasow whama(mono) psuedosymetria dla GABowego
Adam Kazimierz Sieradzan [Fri, 24 Aug 2012 12:07:29 +0000 (08:07 -0400)]
Dzialajaczy dla D aminokwasow whama(mono) psuedosymetria dla GABowego

12 years agopoprawa w Pamread.F dla monochain wham
Adam Kazimierz Sieradzan [Wed, 22 Aug 2012 12:44:08 +0000 (08:44 -0400)]
poprawa w Pamread.F dla monochain wham

12 years agoWham po zmianach i dzialajac dla D aminokwasow i BEZ roznic energi ESTR.
Adam Kazimierz Sieradzan [Fri, 17 Aug 2012 07:00:23 +0000 (03:00 -0400)]
Wham po zmianach i dzialajac dla D aminokwasow i BEZ roznic energi ESTR.

12 years agoRunning D-aminoacid after passed tests. Still problem with
Adam Kazimierz Sieradzan [Tue, 7 Aug 2012 08:34:18 +0000 (04:34 -0400)]
Running D-aminoacid after passed tests. Still problem with
gamsc(21)=1.00d0

12 years agoD i L aminokwasy dzialajace dla src_MD
Adam Kazimierz Sieradzan [Tue, 17 Jul 2012 07:01:49 +0000 (03:01 -0400)]
D i L aminokwasy dzialajace dla src_MD

12 years agoD i L aminokwasy tuz przed testami
Adam Kazimierz Sieradzan [Mon, 9 Jul 2012 07:46:21 +0000 (03:46 -0400)]
D i L aminokwasy tuz przed testami

12 years agoWyrowanie w COmmonie...
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 08:18:36 +0000 (04:18 -0400)]
Wyrowanie w COmmonie...

12 years agozmiana do DiL
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 06:08:43 +0000 (02:08 -0400)]
zmiana do DiL

12 years agoDIL zmiana w param read
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 09:51:00 +0000 (05:51 -0400)]
DIL zmiana w param read

12 years agododanie do gitignor kolejnych moich poligonowy plikow
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 07:51:28 +0000 (03:51 -0400)]
dodanie do gitignor kolejnych moich poligonowy plikow

12 years agoRozgrzebany DIL
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 07:50:05 +0000 (03:50 -0400)]
Rozgrzebany DIL

12 years agofixed broken (by adasko) alignment in COMMON.SCCOR
Dawid Jagiela [Wed, 27 Jun 2012 12:23:49 +0000 (14:23 +0200)]
fixed broken (by adasko) alignment in COMMON.SCCOR

12 years agoMerge branch 'adasko' into devel
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:53:41 +0000 (07:53 -0400)]
Merge branch 'adasko' into devel

Conflicts:
.gitignore
bin/unres/MD/unres_ifort_MPICH_GAB.exe
source/cluster/wham/src/DIMENSIONS.COMPAR
source/cluster/wham/src/Makefile
source/wham/src/Makefile
source/wham/src/cinfo.f
source/wham/src/tmptmp

12 years agoMerge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:40:02 +0000 (07:40 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel

12 years agogit ignore
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:39:16 +0000 (07:39 -0400)]
git ignore

12 years agoglupia zmiana
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:37:49 +0000 (07:37 -0400)]
glupia zmiana

12 years agoWprowadzenie SCCOR do WHAMa i CLUSTROWNIA
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:32:25 +0000 (07:32 -0400)]
Wprowadzenie SCCOR do WHAMa i CLUSTROWNIA

12 years agoLAM/MPI boot ctest modification
Dawid Jagiela [Wed, 20 Jun 2012 20:53:36 +0000 (22:53 +0200)]
LAM/MPI boot ctest modification

12 years agoadded -cpp flag to force preprocesing for all files in gfortran
Dawid Jagiela [Tue, 19 Jun 2012 13:22:11 +0000 (15:22 +0200)]
added -cpp flag to force preprocesing for all files in gfortran

12 years agoMoved ifdef MOMENT part from COMMON.CONTACTS to COMMON.CONTACTS.MOMENT and aplied...
Dawid Jagiela [Tue, 19 Jun 2012 13:04:51 +0000 (15:04 +0200)]
Moved ifdef MOMENT part from COMMON.CONTACTS to COMMON.CONTACTS.MOMENT and aplied preprocesor directives

12 years agoenable compiler preprocesor flags for non-standard files (COMMON.*) in gfortran for...
Dawid Jagiela [Mon, 18 Jun 2012 20:13:38 +0000 (22:13 +0200)]
enable compiler preprocesor flags for non-standard files (COMMON.*) in gfortran for cmake

12 years agoadded source/cluster/wham/src/gnmr1.f to cmake build
Dawid Jagiela [Mon, 18 Jun 2012 19:55:36 +0000 (21:55 +0200)]
added source/cluster/wham/src/gnmr1.f to cmake build

12 years agoadded gnmr1.f to sources in cmake builds
Dawid Jagiela [Mon, 18 Jun 2012 19:42:57 +0000 (21:42 +0200)]
added gnmr1.f to sources in cmake builds

12 years agofixed merge conflict in readrtns_csa.F
Dawid Jagiela [Mon, 18 Jun 2012 19:31:24 +0000 (21:31 +0200)]
fixed merge conflict in readrtns_csa.F

12 years agofixed source/xdrfpdb/src-M/xdrf2pdb-m.F
Dawid Jagiela [Mon, 18 Jun 2012 19:16:05 +0000 (21:16 +0200)]
fixed source/xdrfpdb/src-M/xdrf2pdb-m.F

12 years agofixed merge renamed source file: newconf.f is now newconf.F
Dawid Jagiela [Mon, 18 Jun 2012 19:02:13 +0000 (21:02 +0200)]
fixed merge renamed source file: newconf.f is now newconf.F

12 years agoresolving merge conflicts
Dawid Jagiela [Mon, 18 Jun 2012 18:55:41 +0000 (20:55 +0200)]
resolving merge conflicts

12 years agoMerge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Adam Liwo [Mon, 18 Jun 2012 14:08:46 +0000 (10:08 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
merge adam->devel (2nd attempt)
Conflicts:
.gitignore
bin/unres/MD/unres_ifort_MPICH_GAB.exe
examples/unres/MD/ff_gab/1L2Y_minim.inp
source/cluster/wham/src/DIMENSIONS.COMPAR
source/cluster/wham/src/include_unres/COMMON.INTERACT
source/cluster/wham/src/include_unres/COMMON.SBRIDGE
source/cluster/wham/src/include_unres/COMMON.TORSION
source/unres/src_MD/cinfo.f
source/unres/src_MIN/Makefile
source/xdrfpdb/src-M/xdrf
source/xdrfpdb/src/xdrf
source/xdrfpdb/src/xdrf2ang.f
source/xdrfpdb/src/xdrf2pdb-m.F

12 years agoMerge branch 'adam' into devel
Adam Liwo [Mon, 18 Jun 2012 13:58:32 +0000 (09:58 -0400)]
Merge branch 'adam' into devel
Merging adam with devel
Conflicts:
source/unres/src_CSA/readrtns_csa.F

12 years agofixed indent for gfortran build in source/unres/src_MD/parmread.F
Dawid Jagiela [Mon, 18 Jun 2012 11:25:44 +0000 (13:25 +0200)]
fixed indent for gfortran build in source/unres/src_MD/parmread.F

12 years agoMerge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Mon, 18 Jun 2012 10:46:01 +0000 (12:46 +0200)]
Merge branch 'devel' of mmka:unres into devel

12 years agoremoved MPI form CMakeLists.txt in xdrfpdb
Dawid Jagiela [Mon, 18 Jun 2012 10:43:28 +0000 (12:43 +0200)]
removed MPI form CMakeLists.txt in xdrfpdb
more verbose output in xdrf2pdb-m.F

12 years agounified .gitignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:35:12 +0000 (06:35 -0400)]
unified .gitignore

12 years agosmall fix in .gitingnore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:33:31 +0000 (06:33 -0400)]
small fix in .gitingnore

12 years agoMerge branch 'adasko' into devel
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:22:21 +0000 (06:22 -0400)]
Merge branch 'adasko' into devel

Conflicts:
.gitignore

12 years agopoprawka gitignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:10:09 +0000 (06:10 -0400)]
poprawka gitignore

12 years agozmiana w git ignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:08:32 +0000 (06:08 -0400)]
zmiana w git ignore

12 years agozmiany po usunieciu diagnostyki...
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 09:56:28 +0000 (05:56 -0400)]
zmiany po usunieciu diagnostyki...

12 years ago6/15/2012 by Adam
Adam Liwo [Fri, 15 Jun 2012 19:09:20 +0000 (15:09 -0400)]
6/15/2012 by Adam
Minor changes; linked parallal Makefile in CSA

12 years agodzialajacy grad check....
Adam Kazimierz Sieradzan [Fri, 15 Jun 2012 07:04:52 +0000 (03:04 -0400)]
dzialajacy grad check....

12 years ago6/14/12 by Adam: unnecessary files deleted
Adam Liwo [Thu, 14 Jun 2012 20:20:40 +0000 (16:20 -0400)]
6/14/12 by Adam: unnecessary files deleted

12 years ago6/14/12 by Adam - changes committed
Adam Liwo [Thu, 14 Jun 2012 20:16:07 +0000 (16:16 -0400)]
6/14/12 by Adam - changes committed

12 years ago6/14/2012 by Adam
Adam Liwo [Thu, 14 Jun 2012 20:10:25 +0000 (16:10 -0400)]
6/14/2012 by Adam
1. Fixed a bug in the minimization in angles im all versions; varia
was a simple variable in the calling and a vector in the called subroutine.
2. Removed (wrong) temperature scaling in the CSA snd in the MD version.
3. Added selection of printout information in SUMSL.

12 years agoDzialajacy INTERTYP=1 i INTERTYP=2
Adam Kazimierz Sieradzan [Thu, 14 Jun 2012 11:03:08 +0000 (07:03 -0400)]
Dzialajacy INTERTYP=1 i INTERTYP=2

12 years ago6/11/2012 by Adam
Adam Liwo [Mon, 11 Jun 2012 14:43:15 +0000 (10:43 -0400)]
6/11/2012 by Adam
Yet another revision of xdrf2pdb-m. Error detected in description; directory src-M all pertains to
multi-chain systems (but the programs can also be used for single-chain systems). xdrf2pdb-m for
single-chain systems is in src

12 years ago6/11/2012 by Adam
Adam Liwo [Mon, 11 Jun 2012 14:25:25 +0000 (10:25 -0400)]
6/11/2012 by Adam
xdrf-m corrected (list of arguments); changes in manual required!

12 years agofixed iblnk in xdrf2ang
Dawid Jagiela [Mon, 11 Jun 2012 12:58:33 +0000 (14:58 +0200)]
fixed iblnk in xdrf2ang

12 years agoadded ctests for xdrf2ang
Dawid Jagiela [Mon, 11 Jun 2012 12:34:03 +0000 (14:34 +0200)]
added ctests for xdrf2ang

12 years agofix of malloc in xdrf2pdb-m
Dawid Jagiela [Mon, 11 Jun 2012 12:02:09 +0000 (14:02 +0200)]
fix of malloc in xdrf2pdb-m

12 years agofix of xdrf2ang
Dawid Jagiela [Mon, 11 Jun 2012 11:56:31 +0000 (13:56 +0200)]
fix of xdrf2ang

12 years agoDFA is switched off by default
Cezary Czaplewski [Wed, 9 May 2012 12:02:13 +0000 (14:02 +0200)]
DFA is switched off by default

12 years ago6/11/2012 Changes of the CSA version
Adam Liwo [Mon, 11 Jun 2012 11:07:18 +0000 (07:07 -0400)]
6/11/2012 Changes of the CSA version

12 years ago6/11/2012 Update of the CSA version
Adam Liwo [Mon, 11 Jun 2012 11:06:28 +0000 (07:06 -0400)]
6/11/2012 Update of the CSA version

12 years agoadded ctest/1LE1_mremd_MD000.cx for xdrf2pdb-m testing
Dawid Jagiela [Fri, 8 Jun 2012 11:42:41 +0000 (13:42 +0200)]
added ctest/1LE1_mremd_MD000.cx for xdrf2pdb-m testing

12 years agoxdrf2pdb programs doesn't require MPI so MPI-flags ware removed
Dawid Jagiela [Tue, 5 Jun 2012 14:05:10 +0000 (16:05 +0200)]
xdrf2pdb programs doesn't require MPI so MPI-flags ware removed

12 years agoadded ctests for xdrf2pdb (one & three letter sequence )
Dawid Jagiela [Tue, 5 Jun 2012 13:36:42 +0000 (15:36 +0200)]
added ctests for xdrf2pdb (one & three letter sequence )

12 years agoUNRES single MD for MPI ctest file permissions fix
Dawid Jagiela [Tue, 5 Jun 2012 12:50:33 +0000 (14:50 +0200)]
UNRES single MD for MPI ctest file permissions fix

12 years agoUDALO SIE TERAZ DEBUG
Adam Kazimierz Sieradzan [Tue, 5 Jun 2012 10:40:34 +0000 (06:40 -0400)]
UDALO SIE TERAZ DEBUG

12 years agoadded MPI ctest for unres single MD
Dawid Jagiela [Tue, 5 Jun 2012 09:28:33 +0000 (11:28 +0200)]
added MPI ctest for unres single MD

12 years agokolejna
Adam Kazimierz Sieradzan [Tue, 29 May 2012 12:02:25 +0000 (08:02 -0400)]
kolejna

12 years agozmienionwe zostaly i zostal chyba tylko int to cart deriv
Adam Kazimierz Sieradzan [Tue, 29 May 2012 11:18:45 +0000 (07:18 -0400)]
zmienionwe zostaly i zostal chyba tylko int to cart deriv

12 years agosadas
Adam Kazimierz Sieradzan [Tue, 29 May 2012 09:54:26 +0000 (05:54 -0400)]
sadas

12 years ago5/29/2012 by Adam
Adam Liwo [Tue, 29 May 2012 08:52:17 +0000 (04:52 -0400)]
5/29/2012 by Adam

1. Fixed NaNs in wham (more stable computation of window free energies).
2. Minor fixes in cluster
3. Added exmaple with minimization in MD examples

12 years agocompile_definitions workaround (cmake does not pass it to last file on list) for...
Dawid Jagiela [Sun, 27 May 2012 21:45:02 +0000 (23:45 +0200)]
compile_definitions workaround (cmake does not pass it to last file on list) for  unres/src_MD-M/CMakeLists.txt

12 years agoincluded <stdio.h> in proc_proc.c
Dawid Jagiela [Sun, 27 May 2012 19:19:37 +0000 (21:19 +0200)]
included  <stdio.h> in proc_proc.c

12 years agosscanf EOF fix in source/wham/src-M/proc_proc.c
Dawid Jagiela [Sun, 27 May 2012 19:06:40 +0000 (21:06 +0200)]
sscanf EOF fix in source/wham/src-M/proc_proc.c

12 years agoclosing ascii art frames in energy_p_new.F
Dawid Jagiela [Sun, 27 May 2012 18:56:53 +0000 (20:56 +0200)]
closing ascii art frames in  energy_p_new.F

12 years agoflags typo fix
Dawid Jagiela [Sun, 27 May 2012 18:34:03 +0000 (20:34 +0200)]
flags typo fix

12 years agoadded header for proc_proc.c
Dawid Jagiela [Sat, 26 May 2012 21:51:06 +0000 (23:51 +0200)]
added header for proc_proc.c

12 years agowham compinfo EOF fix
Dawid Jagiela [Sat, 26 May 2012 21:19:02 +0000 (23:19 +0200)]
wham compinfo EOF fix

12 years agoEOF warning fix
Dawid Jagiela [Sat, 26 May 2012 21:12:28 +0000 (23:12 +0200)]
EOF warning fix

12 years agocompinfo.c rewrite
Dawid Jagiela [Sat, 26 May 2012 17:01:29 +0000 (19:01 +0200)]
compinfo.c rewrite

12 years agovoid cast on fgets & fscanf in compinfo.c
Dawid Jagiela [Sat, 26 May 2012 16:25:22 +0000 (18:25 +0200)]
void cast on fgets & fscanf in compinfo.c

12 years agocompinfo.c warning supresion
Dawid Jagiela [Sat, 26 May 2012 15:50:05 +0000 (17:50 +0200)]
compinfo.c warning supresion

12 years agogfortran fix for cluster/wham/src build
Dawid Jagiela [Fri, 25 May 2012 12:16:23 +0000 (14:16 +0200)]
gfortran fix for cluster/wham/src build

12 years agogfortran proc_proc.c build flags fix in source/cluster/wham/src-M
Dawid Jagiela [Thu, 24 May 2012 20:25:15 +0000 (22:25 +0200)]
gfortran proc_proc.c build flags fix in source/cluster/wham/src-M

12 years agointeger overflow fixed in xdrf2x.F
Dawid Jagiela [Tue, 22 May 2012 21:33:00 +0000 (23:33 +0200)]
integer overflow fixed in xdrf2x.F

12 years agomore xdrfpdb fixes for gfortran build
Dawid Jagiela [Tue, 22 May 2012 21:06:12 +0000 (23:06 +0200)]
more xdrfpdb fixes for gfortran build

12 years agogfortran patch for xdrf2ang.f
Dawid Jagiela [Tue, 22 May 2012 20:50:22 +0000 (22:50 +0200)]
gfortran patch for   xdrf2ang.f

12 years agoadded missing source cluster/wham/src-M
Dawid Jagiela [Sun, 20 May 2012 22:07:12 +0000 (00:07 +0200)]
added missing source cluster/wham/src-M

12 years agocluster/wham hc.f gfortran fix
Dawid Jagiela [Sun, 20 May 2012 21:36:29 +0000 (23:36 +0200)]
cluster/wham  hc.f gfortran fix

12 years agoinclude typo fixed + cleanup
Dawid Jagiela [Sun, 20 May 2012 21:16:48 +0000 (23:16 +0200)]
include typo fixed + cleanup

12 years ago5/20/2012 by Adam
Adam Liwo [Sun, 20 May 2012 11:33:15 +0000 (07:33 -0400)]
5/20/2012 by Adam
1. Added distance restraints to wham and cluster
2. Fixed the bug in angle restraints to wham and added angle restraints to cluster
3. Introduced more stable procedure to calculate the dependence of ensemble averages on temperature in wham (for each temperature the lowest "free energy" is a reference to compute Boltzmann factors)

12 years ago deleted: PARAM/1igd.cart~
Dawid Jagiela [Fri, 18 May 2012 11:53:24 +0000 (13:53 +0200)]
deleted:    PARAM/1igd.cart~

12 years agoMerge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Fri, 18 May 2012 11:24:20 +0000 (13:24 +0200)]
Merge branch 'devel' of mmka:unres into devel

12 years agofixed ascii art frames in source/cluster/wham/src-M/energy_p_new.F
Dawid Jagiela [Fri, 18 May 2012 11:23:42 +0000 (13:23 +0200)]
fixed ascii art frames in  source/cluster/wham/src-M/energy_p_new.F

12 years agoMerge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Fri, 18 May 2012 11:17:38 +0000 (13:17 +0200)]
Merge branch 'devel' of mmka:unres into devel

12 years agoan example for MIN only version of unres, corrected paths in Makefile
Cezary Czaplewski [Fri, 18 May 2012 11:16:06 +0000 (13:16 +0200)]
an example for MIN only version of unres, corrected paths in Makefile

12 years agoMerge branch 'feature-cmake' into devel
Dawid Jagiela [Fri, 18 May 2012 11:13:14 +0000 (13:13 +0200)]
Merge branch 'feature-cmake' into devel

12 years agoanother ascii art frame fix
Dawid Jagiela [Fri, 18 May 2012 10:41:17 +0000 (12:41 +0200)]
another ascii art frame fix

12 years agofix for gfortran build of source/cluster/unres
Dawid Jagiela [Fri, 18 May 2012 10:08:31 +0000 (12:08 +0200)]
fix for gfortran build of source/cluster/unres