Cezary Czaplewski [Fri, 24 Feb 2017 06:26:04 +0000 (07:26 +0100)]
cluster wham src-M corrections to match unres energy
Cezary Czaplewski [Fri, 24 Feb 2017 06:08:55 +0000 (07:08 +0100)]
wham src-M corrections to match unres energy
Cezary Czaplewski [Thu, 23 Feb 2017 05:23:24 +0000 (06:23 +0100)]
checkgrad_inc added to input for checkgrad cart
Cezary Czaplewski [Thu, 23 Feb 2017 00:42:52 +0000 (01:42 +0100)]
homology dihederal i-3 gradient correction src_MD
Cezary Czaplewski [Wed, 22 Feb 2017 10:36:13 +0000 (11:36 +0100)]
homology dihederal i-3 gradient correction
Cezary Czaplewski [Wed, 22 Feb 2017 09:38:36 +0000 (10:38 +0100)]
fix checkgrad usampl conflict with homology
Cezary Czaplewski [Wed, 22 Feb 2017 08:32:24 +0000 (09:32 +0100)]
corrections to numerical and sccor analytical gradient
Cezary Czaplewski [Thu, 16 Feb 2017 08:41:06 +0000 (09:41 +0100)]
energy of unres src_MD-M match prerelease
wham and cluster must be changed asap
Cezary Czaplewski [Wed, 14 Sep 2016 13:15:28 +0000 (15:15 +0200)]
increase to 20 max nset waga_homology(20)
Cezary Czaplewski [Tue, 13 Sep 2016 08:50:31 +0000 (10:50 +0200)]
HOMOL_NSET in wham input keyword correction
Cezary Czaplewski [Wed, 24 Aug 2016 20:20:32 +0000 (22:20 +0200)]
Lorentzian restraints on distances in cluster_wham
Cezary Czaplewski [Wed, 24 Aug 2016 13:00:23 +0000 (15:00 +0200)]
Lorentzian restraints on distances in wham
Cezary Czaplewski [Tue, 23 Aug 2016 11:19:16 +0000 (13:19 +0200)]
Lorenz restraints on distances
Cezary Czaplewski [Mon, 4 Jul 2016 17:31:25 +0000 (19:31 +0200)]
multichain debug print removed (no fort.2 file)
Cezary Czaplewski [Mon, 4 Jul 2016 10:31:21 +0000 (12:31 +0200)]
multichain maxres=1000
Cezary Czaplewski [Sun, 26 Jun 2016 13:25:10 +0000 (15:25 +0200)]
wham also in single chain ignores conf. energies>10E6
Cezary Czaplewski [Sun, 19 Jun 2016 14:35:49 +0000 (16:35 +0200)]
correction for idihconstr_end_homo, no differ in wham now
Cezary Czaplewski [Tue, 14 Jun 2016 10:18:17 +0000 (12:18 +0200)]
multichain wham and cluster_wham use readpdb_template
reading of pdb templates the same as in unres/remd code
no diff in energy in wham now
no DEBUG in MREMD to save output space
Cezary Czaplewski [Sat, 11 Jun 2016 17:25:58 +0000 (19:25 +0200)]
correction to the last commit - cleaning of homo restraints
Cezary Czaplewski [Fri, 10 Jun 2016 22:09:49 +0000 (00:09 +0200)]
multichain wham ignores conf. energies>10E6 and speed up of starts
with homo restraints
Cezary Czaplewski [Wed, 8 Jun 2016 12:01:29 +0000 (14:01 +0200)]
single chain correction of dihedral homology restraints phi(i+3)
Cezary Czaplewski [Wed, 8 Jun 2016 10:01:38 +0000 (12:01 +0200)]
unres src_MD max_template=25
Cezary Czaplewski [Wed, 25 May 2016 12:50:36 +0000 (14:50 +0200)]
intel compiler option correction for wham/src-M
Cezary Czaplewski [Thu, 19 May 2016 09:26:32 +0000 (11:26 +0200)]
minim and preminim in cart for large proteins
Cezary Czaplewski [Thu, 19 May 2016 08:12:36 +0000 (10:12 +0200)]
start_from_models working with multichain
Cezary Czaplewski [Thu, 19 May 2016 07:38:09 +0000 (09:38 +0200)]
correction of dihedral homology restraints phi(i+3)
Cezary Czaplewski [Thu, 12 May 2016 17:45:18 +0000 (19:45 +0200)]
MaxT_h=36
Cezary Czaplewski [Thu, 12 May 2016 17:40:37 +0000 (19:40 +0200)]
the first working version of multichain homology
energy is consistend for unres, wham and cluster
but is not the same as for single chain unres
Cezary Czaplewski [Tue, 10 May 2016 19:39:36 +0000 (21:39 +0200)]
PARAM update ext
Cezary Czaplewski [Tue, 10 May 2016 19:34:57 +0000 (21:34 +0200)]
PARAM update ext
Cezary Czaplewski [Tue, 10 May 2016 19:07:23 +0000 (21:07 +0200)]
update of PARAM - new maxliq and ext for src-M parameters
Cezary Czaplewski [Tue, 10 May 2016 18:25:23 +0000 (20:25 +0200)]
updates from src_MD to src_MD-M for unres
Cezary Czaplewski [Thu, 5 May 2016 18:43:38 +0000 (20:43 +0200)]
dfa wham and cluster corrections
Cezary Czaplewski [Thu, 5 May 2016 17:09:44 +0000 (19:09 +0200)]
read2sigma in wham and cluster_wham
some other changes for dfa and energy to match unres
Cezary Czaplewski [Fri, 29 Apr 2016 20:33:23 +0000 (22:33 +0200)]
DIST2_CUT correction
affects also different set of restraints from different models
without DIST2_CUT
Cezary Czaplewski [Fri, 29 Apr 2016 17:46:49 +0000 (19:46 +0200)]
next correction to last commit with DIST2_CUT
Cezary Czaplewski [Fri, 29 Apr 2016 17:39:43 +0000 (19:39 +0200)]
correction to last commit with DIST2_CUT
Cezary Czaplewski [Fri, 29 Apr 2016 17:01:42 +0000 (19:01 +0200)]
DIST2_CUT introduced for homology to remove restraints
Cezary Czaplewski [Thu, 28 Apr 2016 09:28:43 +0000 (11:28 +0200)]
ctest -DUNRES_MPIRUN=1 for tryton
Cezary Czaplewski [Fri, 29 Apr 2016 07:12:36 +0000 (09:12 +0200)]
sigma read from *.sco without 0.5d0*(rescore_tmp+0.5d0)
Cezary Czaplewski [Thu, 28 Apr 2016 21:59:25 +0000 (23:59 +0200)]
mremd with homology constrains can start each replica from random model
add keyword START_FROM_MODELS, works only with READ2SIGMA
and without rest on MD keyword card
Cezary Czaplewski [Thu, 28 Apr 2016 13:04:29 +0000 (15:04 +0200)]
ctest for src-M are off
multichain uses different parameter files
Cezary Czaplewski [Wed, 27 Apr 2016 19:03:45 +0000 (21:03 +0200)]
ctest for empty stat files
Cezary Czaplewski [Wed, 27 Apr 2016 17:39:14 +0000 (19:39 +0200)]
unres_pdb last dummy residue corrected as in prerelease
Cezary Czaplewski [Wed, 27 Apr 2016 16:08:31 +0000 (18:08 +0200)]
ctest copied from prerelease
Cezary Czaplewski [Fri, 22 Apr 2016 17:46:21 +0000 (19:46 +0200)]
cmake -DUNRES_DFA to switch on DFA in unres
Cezary Czaplewski [Tue, 12 Apr 2016 22:13:40 +0000 (00:13 +0200)]
constr_homol corrections in wham and cluster_wham to match unres energy
Cezary Czaplewski [Tue, 12 Apr 2016 20:45:04 +0000 (22:45 +0200)]
wham corrections
Cezary Czaplewski [Fri, 1 Apr 2016 19:25:39 +0000 (21:25 +0200)]
first and last GLY in seq gives correct energy in unres and wham
Conflicts:
source/cluster/wham/src-M/readrtns.F
Cezary Czaplewski [Fri, 18 Mar 2016 02:12:17 +0000 (11:12 +0900)]
arcos = 0.5D0*(PI-DSIGN(1.0D0,X)*PI)
Cezary Czaplewski [Wed, 16 Mar 2016 08:31:50 +0000 (17:31 +0900)]
Adam's corrections to wham
Cezary Czaplewski [Fri, 4 Mar 2016 08:57:37 +0000 (17:57 +0900)]
Adam's changes to wham and cluster following previous commit
XG.. and ..GX sequence is automatically corrected
also in cluster_wham it is possible to select number of clusters
instead of cutoff
Cezary Czaplewski [Fri, 4 Mar 2016 07:36:50 +0000 (16:36 +0900)]
Adam's changes to avoid wrong XG.. or ..GX sequence input
Cezary Czaplewski [Thu, 3 Mar 2016 05:51:29 +0000 (06:51 +0100)]
max_template instead of fix number 19 in wham and cluster
Cezary Czaplewski [Thu, 3 Mar 2016 05:37:25 +0000 (06:37 +0100)]
corrections to changes form nostromo
Cezary Czaplewski [Thu, 3 Mar 2016 03:57:04 +0000 (12:57 +0900)]
changes from nostromo
Cezary Czaplewski [Thu, 25 Feb 2016 06:49:58 +0000 (15:49 +0900)]
default iset in cluster_wham set to 1
Cezary Czaplewski [Thu, 25 Feb 2016 04:34:18 +0000 (05:34 +0100)]
some corrections to previous commit from nostromo
now compiles on piasek4 with ifort
Cezary Czaplewski [Thu, 25 Feb 2016 03:54:22 +0000 (12:54 +0900)]
Adam's changes from nostromo to wham with homology
Cezary Czaplewski [Wed, 17 Feb 2016 11:52:09 +0000 (12:52 +0100)]
correction for homol_nset>1 and waga_homology(iset)=0 to prevent sigsegv
Cezary Czaplewski [Thu, 28 Jan 2016 21:51:10 +0000 (22:51 +0100)]
compilation of large cluster_wham with -mcmodel=medium -shared-intel
Cezary Czaplewski [Thu, 28 Jan 2016 21:12:19 +0000 (22:12 +0100)]
compilation of large wham with -mcmodel=medium -shared-intel
Cezary Czaplewski [Thu, 28 Jan 2016 19:43:06 +0000 (20:43 +0100)]
correction to cluter_wham
Cezary Czaplewski [Thu, 28 Jan 2016 16:16:44 +0000 (17:16 +0100)]
cleaning (links and backup files)
Cezary Czaplewski [Thu, 28 Jan 2016 15:56:14 +0000 (16:56 +0100)]
wham with mpich2 (no aliasing) and new dimenstions
Cezary Czaplewski [Thu, 28 Jan 2016 10:55:30 +0000 (11:55 +0100)]
max_template=25
Cezary Czaplewski [Thu, 28 Jan 2016 10:46:28 +0000 (11:46 +0100)]
all CMakeLists.txt updated with corrected names and directories
Cezary Czaplewski [Thu, 28 Jan 2016 10:11:25 +0000 (11:11 +0100)]
correction - adding ehomology_constr
Cezary Czaplewski [Mon, 30 Nov 2015 11:28:52 +0000 (12:28 +0100)]
Ehomology printout with PRINT_COMPON
Cezary Czaplewski [Mon, 30 Nov 2015 09:01:06 +0000 (10:01 +0100)]
timlim function ovrtim only on master and MPI_Bcast
Cezary Czaplewski [Sun, 22 Nov 2015 10:45:14 +0000 (11:45 +0100)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Cezary Czaplewski [Sun, 22 Nov 2015 10:43:36 +0000 (11:43 +0100)]
CONSTR_HOMOL in mutlichain, debug and output cleaning
Cezary Czaplewski [Tue, 27 Oct 2015 13:26:08 +0000 (14:26 +0100)]
printmat added to cmake
Cezary Czaplewski [Tue, 27 Oct 2015 08:45:19 +0000 (09:45 +0100)]
ENERGY_DEC printout works for ESTR
Cezary Czaplewski [Mon, 26 Oct 2015 11:45:46 +0000 (12:45 +0100)]
ENERGY_DEC printout works for ebend in E0LL2Y forcefield
Cezary Czaplewski [Fri, 23 Oct 2015 13:04:16 +0000 (15:04 +0200)]
preminim in multichain code
Cezary Czaplewski [Tue, 20 Oct 2015 18:26:08 +0000 (20:26 +0200)]
changes to avoid problems with MPI_Scatterv in mpich2 for FGPROC>1
Cezary Czaplewski [Tue, 20 Oct 2015 17:13:26 +0000 (19:13 +0200)]
Adasko's changes to ebend
Cezary Czaplewski [Thu, 8 Oct 2015 20:39:19 +0000 (22:39 +0200)]
energy_dec works with etors_d
Cezary Czaplewski [Tue, 6 Oct 2015 14:40:17 +0000 (16:40 +0200)]
unres src_MD-M from branch Multichain
Cezary Czaplewski [Wed, 30 Sep 2015 13:26:20 +0000 (15:26 +0200)]
cmake is working for cluster_unres
Adam Liwo [Wed, 30 Sep 2015 10:05:39 +0000 (12:05 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Adam Liwo [Wed, 30 Sep 2015 10:02:39 +0000 (12:02 +0200)]
Added main_clust.F
Cezary Czaplewski [Wed, 30 Sep 2015 09:47:39 +0000 (11:47 +0200)]
Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology
Cezary Czaplewski [Wed, 30 Sep 2015 09:27:24 +0000 (11:27 +0200)]
cutoff for dfa beta formation to speed up calculations
Adam Liwo [Tue, 15 Sep 2015 12:45:25 +0000 (14:45 +0200)]
Added newly created cluster exe and makefile
Adam Liwo [Tue, 11 Aug 2015 13:43:17 +0000 (15:43 +0200)]
Minor change in unres-cluster DIMENSIONS
Adam Liwo [Tue, 11 Aug 2015 04:09:06 +0000 (06:09 +0200)]
Cluster/unres modified to read MD coordinates in CX format, also from multiple files.
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