unres.git
8 years agoExtended maximum residue number and number of temperatures.
Pawel Krupa [Sun, 15 May 2016 18:37:37 +0000 (14:37 -0400)]
Extended maximum residue number and number of temperatures.

8 years agoMemory overflow correction.
Pawel Krupa [Sat, 14 May 2016 22:20:05 +0000 (00:20 +0200)]
Memory overflow correction.

8 years agoNumber of temperatures in WHAM changed from 32 to 36 and WHPB name changed to WSTRAIN...
Pawel Krupa [Sat, 14 May 2016 21:57:54 +0000 (17:57 -0400)]
Number of temperatures in WHAM changed from 32 to 36 and WHPB name changed to WSTRAIN (to be the same as in UNRES and cluster).

8 years agoctest -DUNRES_MPIRUN=1 for tryton
Cezary Czaplewski [Thu, 28 Apr 2016 09:28:43 +0000 (11:28 +0200)]
ctest -DUNRES_MPIRUN=1 for tryton

8 years agocmake -mcmodel=medium for gfortran wham and cluster_wham
Cezary Czaplewski [Thu, 28 Apr 2016 06:07:03 +0000 (08:07 +0200)]
cmake -mcmodel=medium for gfortran wham and cluster_wham

8 years agoctest for empty stat files
Cezary Czaplewski [Wed, 27 Apr 2016 19:03:45 +0000 (21:03 +0200)]
ctest for empty stat files

8 years agoAddition to the last commit.
Pawel Krupa [Wed, 27 Apr 2016 14:33:26 +0000 (16:33 +0200)]
Addition to the last commit.

8 years agoAdded maxlik potentials for CASP12 and protein dimensions has been set to 800 residue...
Pawel Krupa [Wed, 27 Apr 2016 14:29:53 +0000 (16:29 +0200)]
Added maxlik potentials for CASP12 and protein dimensions has been set to 800 residues in wham and cluster.

8 years agoctest relax test criteria
Cezary Czaplewski [Wed, 27 Apr 2016 11:29:56 +0000 (13:29 +0200)]
ctest relax test criteria

8 years agoAIX xdrfint_
Cezary Czaplewski [Mon, 25 Apr 2016 21:01:00 +0000 (23:01 +0200)]
AIX xdrfint_

8 years agoctest correct path for xdrf2* tools
Cezary Czaplewski [Mon, 25 Apr 2016 17:22:30 +0000 (19:22 +0200)]
ctest correct path for xdrf2* tools

8 years agoctest on cray with srun all tests
Cezary Czaplewski [Mon, 25 Apr 2016 16:18:34 +0000 (18:18 +0200)]
ctest on cray with srun all tests

8 years agoctest on cray with srun
Cezary Czaplewski [Mon, 25 Apr 2016 15:56:35 +0000 (17:56 +0200)]
ctest on cray with srun

8 years agoctest csa for E0LL2Y
Cezary Czaplewski [Fri, 22 Apr 2016 09:32:28 +0000 (11:32 +0200)]
ctest csa for E0LL2Y

8 years agoctest works with lam mpi
Cezary Czaplewski [Mon, 18 Apr 2016 12:56:38 +0000 (14:56 +0200)]
ctest works with lam mpi

8 years agofirst and last GLY in seq gives correct energy in unres and wham
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

8 years ago1st GLY in seq gives correct energy in unres and wham
Cezary Czaplewski [Fri, 1 Apr 2016 13:04:17 +0000 (15:04 +0200)]
1st GLY in seq gives correct energy in unres and wham

8 years agoctest the first static disulfide test ene/min cart
Cezary Czaplewski [Thu, 24 Mar 2016 14:53:10 +0000 (15:53 +0100)]
ctest the first static disulfide test ene/min cart

8 years agocluster_wham src-M agrees with src for single chain
Cezary Czaplewski [Thu, 24 Mar 2016 02:08:05 +0000 (03:08 +0100)]
cluster_wham src-M agrees with src for single chain

8 years agoctest wham and cluster_wham correction
Cezary Czaplewski [Thu, 24 Mar 2016 00:47:33 +0000 (01:47 +0100)]
ctest wham and cluster_wham correction

8 years agowham & cluster_wham energy correction to match unres src_MD
Cezary Czaplewski [Wed, 23 Mar 2016 21:55:00 +0000 (22:55 +0100)]
wham & cluster_wham energy correction to match unres src_MD

8 years agowham thermal format $ correction for gfortran
Cezary Czaplewski [Wed, 23 Mar 2016 02:41:17 +0000 (03:41 +0100)]
wham thermal format $ correction for gfortran

8 years agoctest microcanoninal energy fluctuations limits adjusted
Cezary Czaplewski [Wed, 23 Mar 2016 01:25:43 +0000 (02:25 +0100)]
ctest microcanoninal energy fluctuations limits adjusted

8 years agoimax0 replaced with max0
Cezary Czaplewski [Tue, 22 Mar 2016 14:38:28 +0000 (15:38 +0100)]
imax0 replaced with max0

imax0 uses integer*2 and is not implemented in gfortran

8 years agoctest wham checks energy differs
Cezary Czaplewski [Tue, 22 Mar 2016 06:19:19 +0000 (07:19 +0100)]
ctest wham checks energy differs

8 years agoctest multichain protein-peptide complex
Cezary Czaplewski [Tue, 22 Mar 2016 05:36:44 +0000 (06:36 +0100)]
ctest multichain protein-peptide complex

8 years agoMerge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Cezary Czaplewski [Tue, 22 Mar 2016 03:49:33 +0000 (04:49 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

8 years agoenergy_dec for esccor and some other debug printout
Cezary Czaplewski [Tue, 22 Mar 2016 03:48:24 +0000 (04:48 +0100)]
energy_dec for esccor and some other debug printout

8 years agoMerge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Cezary Czaplewski [Fri, 18 Mar 2016 02:13:36 +0000 (11:13 +0900)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

8 years agoarcos = 0.5D0*(PI-DSIGN(1.0D0,X)*PI)
Cezary Czaplewski [Fri, 18 Mar 2016 02:12:17 +0000 (11:12 +0900)]
arcos = 0.5D0*(PI-DSIGN(1.0D0,X)*PI)

8 years agoAdam's corrections to wham from homology branch
Cezary Czaplewski [Thu, 17 Mar 2016 01:28:39 +0000 (10:28 +0900)]
Adam's corrections to wham from homology branch

8 years agosrc_MIN sum_gradient from src_MD
Cezary Czaplewski [Tue, 15 Mar 2016 04:35:16 +0000 (13:35 +0900)]
src_MIN sum_gradient from src_MD

8 years agonosearchsc in src_MIN as in other versions
Cezary Czaplewski [Tue, 15 Mar 2016 04:15:35 +0000 (05:15 +0100)]
nosearchsc in src_MIN as in other versions

8 years agosrc_MIN eback_sc_corr do intertyp=1,3
Cezary Czaplewski [Tue, 15 Mar 2016 02:02:58 +0000 (11:02 +0900)]
src_MIN eback_sc_corr do intertyp=1,3

8 years agoctest added ene tests with FGPROCS=1
Cezary Czaplewski [Tue, 15 Mar 2016 01:55:11 +0000 (02:55 +0100)]
ctest added ene tests with FGPROCS=1

8 years agoctest update of ref energy with correct sccor values
Cezary Czaplewski [Tue, 15 Mar 2016 01:28:43 +0000 (02:28 +0100)]
ctest update of ref energy with correct sccor values

8 years agolast corrections copied to src_MD-M
Cezary Czaplewski [Mon, 14 Mar 2016 06:59:54 +0000 (15:59 +0900)]
last corrections copied to src_MD-M

8 years agocorretion .ge.-pi instead of .gt.-pi in intcartderiv
Cezary Czaplewski [Mon, 14 Mar 2016 06:41:41 +0000 (15:41 +0900)]
corretion .ge.-pi instead of .gt.-pi in intcartderiv

8 years agoeback_sc_corr do intertyp=1,3
Cezary Czaplewski [Mon, 14 Mar 2016 06:27:07 +0000 (15:27 +0900)]
eback_sc_corr  do intertyp=1,3

8 years agoctest wsccor 0.25 wtor 1.34316 in all tests
Cezary Czaplewski [Mon, 14 Mar 2016 02:32:51 +0000 (03:32 +0100)]
ctest wsccor 0.25 wtor 1.34316 in all tests

8 years agoctest ENE changed to minimize unres_pdb structure
Cezary Czaplewski [Sat, 12 Mar 2016 03:39:21 +0000 (04:39 +0100)]
ctest ENE changed to minimize unres_pdb structure

native pdb had too large vdw energy which can cover
changes of other energy components

8 years agoctest cluster int for csa output
Cezary Czaplewski [Fri, 11 Mar 2016 06:49:33 +0000 (07:49 +0100)]
ctest cluster int for csa output

8 years agocmake corrections to unres/src_MIN
Cezary Czaplewski [Fri, 11 Mar 2016 05:08:34 +0000 (06:08 +0100)]
cmake corrections to unres/src_MIN

8 years agocorrections to unres src_MIN
Cezary Czaplewski [Thu, 10 Mar 2016 17:14:51 +0000 (18:14 +0100)]
corrections to unres src_MIN

8 years agoctest unres src_MIN and changes for the same energy as src_MD
Cezary Czaplewski [Thu, 10 Mar 2016 16:29:30 +0000 (17:29 +0100)]
ctest unres src_MIN and changes for the same energy as src_MD

8 years agoctest cluster_wham src-M
Cezary Czaplewski [Thu, 10 Mar 2016 15:16:41 +0000 (16:16 +0100)]
ctest cluster_wham src-M

8 years agoctest correction to previous commit
Cezary Czaplewski [Thu, 10 Mar 2016 14:39:21 +0000 (15:39 +0100)]
ctest correction to previous commit

8 years agoctest cluster_wham
Cezary Czaplewski [Thu, 10 Mar 2016 14:35:06 +0000 (15:35 +0100)]
ctest cluster_wham

8 years agocleaning of cluster_wham
Cezary Czaplewski [Thu, 10 Mar 2016 13:48:29 +0000 (14:48 +0100)]
cleaning of cluster_wham

8 years agocorrection after cherry-pick and merge in last commit
Cezary Czaplewski [Thu, 10 Mar 2016 11:52:44 +0000 (20:52 +0900)]
correction after cherry-pick and merge in last commit

8 years agoAdam's changes to wham and cluster following previous commit
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

Conflicts:
source/cluster/wham/src/COMMON.CONTROL
source/cluster/wham/src/energy_p_new.F
source/cluster/wham/src/probabl.F
source/cluster/wham/src/readpdb.F
source/cluster/wham/src/readrtns.F
source/wham/src/energy_p_new.F

8 years agocorrections to cluster_wham
Cezary Czaplewski [Thu, 10 Mar 2016 07:39:48 +0000 (08:39 +0100)]
corrections to cluster_wham

8 years agowham src-M correction to make it working
Cezary Czaplewski [Thu, 10 Mar 2016 07:03:16 +0000 (16:03 +0900)]
wham src-M correction to make it working

8 years agocorrection to previous commit again
Cezary Czaplewski [Thu, 10 Mar 2016 06:49:08 +0000 (15:49 +0900)]
correction to previous commit again

8 years agocorrection to previous commit
Cezary Czaplewski [Thu, 10 Mar 2016 06:19:21 +0000 (15:19 +0900)]
correction to previous commit

8 years agoctest wham in src-M
Cezary Czaplewski [Thu, 10 Mar 2016 06:18:24 +0000 (15:18 +0900)]
ctest wham in src-M

8 years agoMerge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Cezary Czaplewski [Thu, 10 Mar 2016 05:54:46 +0000 (14:54 +0900)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

8 years agoctest wham
Cezary Czaplewski [Thu, 10 Mar 2016 05:53:51 +0000 (14:53 +0900)]
ctest wham

8 years agorevert DIMENSIONS corrected maxterm_sccor=6
Cezary Czaplewski [Thu, 10 Mar 2016 04:51:24 +0000 (05:51 +0100)]
revert DIMENSIONS corrected maxterm_sccor=6

error was in wham COMMON.SCCOR

8 years agoMerge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Cezary Czaplewski [Thu, 10 Mar 2016 03:58:50 +0000 (04:58 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

8 years agowham cmake ifort options for larger data
Cezary Czaplewski [Thu, 10 Mar 2016 03:57:03 +0000 (12:57 +0900)]
wham cmake ifort options for larger data

8 years agoDIMENSIONS corrected maxterm_sccor=20
Cezary Czaplewski [Thu, 10 Mar 2016 03:49:58 +0000 (04:49 +0100)]
DIMENSIONS corrected maxterm_sccor=20

8 years agoctest update for src_MD-M test to match src_MD
Cezary Czaplewski [Wed, 9 Mar 2016 08:27:37 +0000 (17:27 +0900)]
ctest update for src_MD-M test to match src_MD

8 years agoctest corrections to mpi script and remd test
Cezary Czaplewski [Wed, 9 Mar 2016 08:04:01 +0000 (09:04 +0100)]
ctest corrections to mpi script and remd test

8 years agoctest for remd
Cezary Czaplewski [Wed, 9 Mar 2016 07:17:51 +0000 (08:17 +0100)]
ctest for remd

checks average ACC, plots histograms of energy for each bath
temperature and energy v.s bath temperature

8 years agominimization in internal coordinates works in src_MD-M
Cezary Czaplewski [Wed, 9 Mar 2016 04:43:12 +0000 (13:43 +0900)]
minimization in internal coordinates works in src_MD-M

8 years agoctest correction to previous commit
Cezary Czaplewski [Wed, 9 Mar 2016 02:49:44 +0000 (03:49 +0100)]
ctest correction to previous commit

8 years agoctest for Nose-Hoover removed from srcMD-M
Cezary Czaplewski [Wed, 9 Mar 2016 00:49:29 +0000 (01:49 +0100)]
ctest for Nose-Hoover removed from srcMD-M

there is no code for this thermostat in srcMD-M

8 years agocorrections to src_MD-M for the same energy as src_MD
Cezary Czaplewski [Tue, 8 Mar 2016 09:03:24 +0000 (18:03 +0900)]
corrections to src_MD-M for the same energy as src_MD

8 years agoctest for src_MD-M copied from src_MD
Cezary Czaplewski [Tue, 8 Mar 2016 07:25:33 +0000 (08:25 +0100)]
ctest for src_MD-M copied from src_MD

8 years agoctest local csa added with 4P force field
Cezary Czaplewski [Tue, 8 Mar 2016 05:18:55 +0000 (06:18 +0100)]
ctest local csa added with 4P force field

8 years agoctest correction to previous commit
Cezary Czaplewski [Tue, 8 Mar 2016 02:12:10 +0000 (03:12 +0100)]
ctest correction to previous commit

8 years agoctest for thermostats: Langevin, Nose-Hoover and Berendsen
Cezary Czaplewski [Tue, 8 Mar 2016 01:28:55 +0000 (02:28 +0100)]
ctest for thermostats: Langevin, Nose-Hoover and Berendsen

with plotting of temperature distribution using python matplotlib

8 years agoAdam's changes to avoid wrong XG.. or ..GX sequence input
Cezary Czaplewski [Fri, 4 Mar 2016 07:36:50 +0000 (16:36 +0900)]
Adam's changes to avoid wrong XG.. or ..GX sequence input

8 years agoctest tolerance for csa emin inreased to 5.0
Cezary Czaplewski [Fri, 4 Mar 2016 04:18:00 +0000 (05:18 +0100)]
ctest tolerance for csa emin inreased to 5.0

8 years agoctest for CSA global with 4P force field
Cezary Czaplewski [Wed, 2 Mar 2016 07:43:25 +0000 (08:43 +0100)]
ctest for CSA global with 4P force field

8 years agoctest works with lam and mpich
Cezary Czaplewski [Wed, 2 Mar 2016 05:03:12 +0000 (06:03 +0100)]
ctest works with lam and mpich

8 years agoctest for internal coordinates and regular minimization
Cezary Czaplewski [Wed, 2 Mar 2016 03:06:10 +0000 (04:06 +0100)]
ctest for internal coordinates and regular minimization

8 years agoctest for minimization and microcanonical MD
Cezary Czaplewski [Mon, 29 Feb 2016 09:34:10 +0000 (10:34 +0100)]
ctest for minimization and microcanonical MD

test of minimization of protein A compares final energy and SUMSL return code
test of microcanonical MD of 1L2Y calculates average total energy and its standard deviation

8 years agocorrection to previous commit CTEST_FULL_OUTPUT
Cezary Czaplewski [Mon, 29 Feb 2016 05:36:08 +0000 (06:36 +0100)]
correction to previous commit CTEST_FULL_OUTPUT

8 years agoadded echo CTEST_FULL_OUTPUT (Avoid ctest truncation of output)
Cezary Czaplewski [Mon, 29 Feb 2016 05:27:04 +0000 (06:27 +0100)]
added echo CTEST_FULL_OUTPUT (Avoid ctest truncation of output)

8 years agoctest for E0LL2Y with MPI now using FGPROCS=2
Cezary Czaplewski [Mon, 29 Feb 2016 05:06:39 +0000 (06:06 +0100)]
ctest for E0LL2Y with MPI now using FGPROCS=2

8 years agoctest for E0LL2Y with reference energy diff
Cezary Czaplewski [Mon, 29 Feb 2016 03:45:56 +0000 (04:45 +0100)]
ctest for E0LL2Y with reference energy diff

8 years agoadding correction in cluster debug
Adam Sieradzan [Thu, 11 Feb 2016 07:21:25 +0000 (08:21 +0100)]
adding correction in cluster debug

8 years agoMerge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Adam Liwo [Sun, 20 Dec 2015 19:02:54 +0000 (20:02 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

8 years agoFized same buffer issue in gather and gatherv in wham and cluster and a minor issue...
Adam Liwo [Fri, 18 Dec 2015 19:29:56 +0000 (20:29 +0100)]
Fized same buffer issue in gather and gatherv in wham and cluster and a minor issue in initialize

8 years agoxdrf added to cluster
Adam Liwo [Thu, 26 Nov 2015 20:01:06 +0000 (21:01 +0100)]
xdrf added to cluster

9 years agoENERGY_DEC printout works for ESTR
Cezary Czaplewski [Tue, 27 Oct 2015 08:45:19 +0000 (09:45 +0100)]
ENERGY_DEC printout works for ESTR

9 years ago ENERGY_DEC printout works for ebend in E0LL2Y forcefield
Cezary Czaplewski [Mon, 26 Oct 2015 11:13:10 +0000 (12:13 +0100)]
 ENERGY_DEC printout works for ebend in E0LL2Y forcefield

9 years agoswitch off debugging in src_MD-M
Cezary Czaplewski [Wed, 14 Oct 2015 16:24:45 +0000 (18:24 +0200)]
switch off debugging in src_MD-M

9 years agoenergy_dec works with etors_d
Cezary Czaplewski [Thu, 8 Oct 2015 20:39:19 +0000 (22:39 +0200)]
energy_dec works with etors_d

Conflicts:

source/unres/src_MD-M/energy_p_new_barrier.F

9 years agoChanges AL
Adam Liwo [Wed, 30 Sep 2015 09:45:45 +0000 (11:45 +0200)]
Changes AL

9 years agorestraints from contact prediction for CSA version
Cezary Czaplewski [Tue, 7 Jul 2015 07:31:37 +0000 (09:31 +0200)]
restraints from contact prediction for CSA version

9 years agoby Adam
Adam Liwo [Fri, 5 Jun 2015 20:35:08 +0000 (22:35 +0200)]
by Adam

9 years agoImport fixed makefiles in cluster
Adam Liwo [Sun, 10 May 2015 02:44:22 +0000 (04:44 +0200)]
Import fixed makefiles in cluster
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

Conflicts:
source/cluster/wham/src-M/Makefile-MPICH-gfortran
source/cluster/wham/src-M/Makefile-MPICH-ifort

9 years agoFixed geomout.F
Adam Liwo [Sun, 10 May 2015 02:34:55 +0000 (04:34 +0200)]
Fixed geomout.F

9 years agoMerge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Adam Liwo [Sun, 10 May 2015 02:31:17 +0000 (04:31 +0200)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

Conflicts:
source/unres/src_MD/intcartderiv.F

9 years agoadding in cmake UNRES_MD_FF = 4P for wham and cluster
Cezary Czaplewski [Thu, 7 May 2015 04:52:11 +0000 (06:52 +0200)]
adding in cmake UNRES_MD_FF = 4P for wham and cluster

9 years agoadding in cmake UNRES_MD_FF = 4P for src_MD and src_MD-M
Cezary Czaplewski [Thu, 7 May 2015 04:33:23 +0000 (06:33 +0200)]
adding in cmake UNRES_MD_FF = 4P for src_MD and src_MD-M

9 years agofixed binary names for cmake (update)
Cezary Czaplewski [Thu, 7 May 2015 04:02:37 +0000 (06:02 +0200)]
fixed binary names for cmake (update)