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Fixed bug in orires code that was checking too strict.
2020-02-20
D
a
vid va
n
der Spoel
Fi
x
ed bug i
n
orires
code
that wa
s
c
h
e
c
king t
o
o strict
.
commit
|
commitdiff
|
tree
2020-02-18
David va
n
der Sp
o
el
Fixed typo in G
M
XRC
.
c
s
h
.
cmakein
commit
|
commitdiff
|
tree
2019-07-09
David van der S
p
oel
Fix
e
d
sm
a
ll bug in g
m
x
a
naeig
commit
|
commitdiff
|
tree
2019-04-05
David van der Spoel
Fixed manual for dihedral re
s
traints
.
commit
|
commitdiff
|
tree
2019-03-31
Davi
d
v
a
n der
S
p
oel
Removed confu
s
ing gpp_atomtype functions
.
commit
|
commitdiff
|
tree
2019-02-18
Da
v
id
v
an der Spoel
Prec
i
sion
f
i
x for rescbt co
d
e
.
commit
|
commitdiff
|
tree
2019-02-16
David va
n
der Spoel
Tes
t
s of restrained listed potentials
.
commit
|
commitdiff
|
tree
2019-02-11
Dav
i
d van der Spo
e
l
Remove
b
uggy debug output
.
commit
|
commitdiff
|
tree
2019-02-11
David
v
a
n
der Sp
o
el
Tests for pol
a
rizatio
n
functions
.
commit
|
commitdiff
|
tree
2019-02-08
Davi
d
van d
e
r Spoel
Furt
h
er incr
e
ase of tolerance for angles
.
commit
|
commitdiff
|
tree
2019-02-08
David
van
d
er Spoe
l
Increased tolerance for
a
ngle functi
o
ns
.
commit
|
commitdiff
|
tree
2019-02-08
David van der Spoe
l
Increase t
o
lerance in Angle test
.
commit
|
commitdiff
|
tree
2019-02-08
David van der
S
poel
T
ests
f
or l
i
ste
d
force potentials
.
commit
|
commitdiff
|
tree
2019-01-26
D
a
vid van der Spo
e
l
Fixed some typos
in commen
t
s
.
commit
|
commitdiff
|
tree
2019-01-17
David v
a
n de
r
Spoe
l
Allow multiple
coordinate sets in l
i
sted_
f
orces
t
est
.
commit
|
commitdiff
|
tree
2019-01-17
Davi
d
v
a
n de
r
Sp
o
el
Mov
e
d one regression
t
est t
o
c
ore grom
a
cs
.
commit
|
commitdiff
|
tree
2019-01-14
David van
d
er Spoel
MSD t
e
sts for the -mol option
.
commit
|
commitdiff
|
tree
2019-01-11
D
a
vid van de
r
S
p
o
e
l
Added low-level
t
e
s
t
s
f
or im
p
rop
e
r dihedrals
.
commit
|
commitdiff
|
tree
2018-12-31
D
avid van
der S
p
oe
l
Move
d
g
ene
r
ic s
i
m
ulationdat
a
base
c
ode to testut
i
l
s
.
commit
|
commitdiff
|
tree
2018-12-30
Da
v
i
d v
a
n
der
S
p
o
el
Moved input fil
e
s for test
s
to
simulation
d
a
tabas
e
.
commit
|
commitdiff
|
tree
2018-12-30
David van der Sp
o
el
Implemented na
t
ive
n
o
rmal mode analysis te
s
ts
.
commit
|
commitdiff
|
tree
2018-12-22
David van der
S
poel
Revert "
R
em
o
ved t
_
topology from gmx msd"
commit
|
commitdiff
|
tree
2018-12-20
David van
der Spoe
l
Remove
d
t_to
p
ology from g
m
x m
s
d
commit
|
commitdiff
|
tree
2018-12-05
Da
v
id van der Spoel
Added new
t
esting code for normal mode analysis
.
commit
|
commitdiff
|
tree
2018-12-04
Da
v
id van
der Spoel
Smal
l
u
pd
a
t
e
to mdrun tes
t
s
.
commit
|
commitdiff
|
tree
2018-12-04
David v
a
n der Spo
e
l
Removed
gmx morph
commit
|
commitdiff
|
tree
2018-12-04
David van de
r
Spoel
Rem
o
v
ed gm
x
dyndom
commit
|
commitdiff
|
tree
2018-12-04
David van
der
Spoel
Removed gm
x
a
n
a
dock
commit
|
commitdiff
|
tree
2018-11-21
David van der Spoel
Merg
e
branch 'release-2019'
commit
|
commitdiff
|
tree
2018-11-18
David
v
an der Spoel
Added citatio
n
for new analysis f
u
nction
a
lity
.
commit
|
commitdiff
|
tree
2018-11-11
David van der Spoel
Fi
x
entropy ca
l
culation i
n
gmx anae
i
g
commit
|
commitdiff
|
tree
2018-11-09
D
a
vid van der Spoel
Change ge
t
_atom_index to allow
multiple molecules
.
commit
|
commitdiff
|
tree
2018-10-11
David va
n
d
er Spo
e
l
Reinstated
q
uasiharm
o
nic en
t
ropy calcula
t
ion in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
David
van
d
er Spoel
Added op
t
ion to gmx
nmeig to pr
i
nt
Z
PE
.
commit
|
commitdiff
|
tree
2018-06-12
Da
v
id van der Spoe
l
Le
t
gmx
n
meig print
thermochemist
r
y
.
commit
|
commitdiff
|
tree
2018-03-21
David va
n
der Spoel
Renamed
entropy
.
* to thermoch
e
mistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van d
e
r S
p
oel
Split
o
f
f entropy ca
l
culatio
n
to sep
a
rate file
.
commit
|
commitdiff
|
tree
2017-12-28
David v
a
n der Spoel
F
i
xes and upd
a
te
s
for x
p
lo
r
2gml
.
pl and
atom_
n
om
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van
der Spoel
Fixed c
h
e
c
k for w
a
ter in
g
e
n_vsite
.
cp
p
commit
|
commitdiff
|
tree
2017-11-02
David
v
an der Spoel
New mdp input
for
e
l
e
ctric fiel
d
s
.
commit
|
commitdiff
|
tree
2017-10-30
Davi
d
van
d
er Spo
e
l
Fixed mdp ou
t
put from electric
f
ield code
.
commit
|
commitdiff
|
tree
2017-10-30
D
a
v
id van der S
p
oel
Added option -wate
r
tips3p to
p
db2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
D
a
vid van der Spoel
S
p
lit off the NMR related
anal
y
s
e
s from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
Davi
d
v
a
n der Spoe
l
Fixed missin
g
entries in nrnb arrays
.
commit
|
commitdiff
|
tree
2017-08-15
D
a
vi
d
va
n
der Spoe
l
Worked around missi
n
g OpenMP im
p
lementatio
n
in
orires
.
commit
|
commitdiff
|
tree
2017-08-03
D
avid van
d
er Spo
e
l
Fixed bug in gmx disres
i
ndexing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
D
avid van der Sp
o
el
Worked aro
u
nd
missing Op
e
n
M
P
implementation
in orires
.
commit
|
commitdiff
|
tree
2017-07-28
D
av
i
d va
n
der Spoel
Ad
d
e
d un
i
t-
t
est for orientat
i
on restraints
ou
t
p
ut
.
commit
|
commitdiff
|
tree
2017-07-19
David van der S
p
o
e
l
Rem
o
ve
d
unne
c
essary static dec
l
arations for
c
ommand
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Sp
o
el
Fixed test-order dependenc
y
i
n gmxpreprocess t
e
sts
.
commit
|
commitdiff
|
tree
2017-07-19
Dav
i
d van
der
Sp
o
el
Fix non-r
e
producability of clustsi
z
e tests
.
commit
|
commitdiff
|
tree
2017-05-01
D
a
vid van
d
e
r Spo
e
l
Xpm test for gmx clus
t
s
i
ze
commit
|
commitdiff
|
tree
2017-03-12
D
avid van der
Spoel
Added
tes
t
s for gmx
c
lustsize
.
commit
|
commitdiff
|
tree
2017-03-04
D
avid van
d
er
Spoel
Removes rogu
e
pr
i
nting to xvg file in gmx
m
i
ndis
t
commit
|
commitdiff
|
tree
2017-02-27
Dav
i
d van der Spoel
Fixes b
u
g
in g
m
x solvate with -shell that yielded
0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
D
avi
d
van der Spoel
F
ix
e
s SEGV in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
David va
n
der Spoel
Onl
y
p
r
int all dangling atoms with
grom
p
p -v
commit
|
commitdiff
|
tree
2017-01-23
D
avid van der Spo
e
l
Added reference for dih
e
dral f
u
nction
in
OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David v
a
n der
S
poel
Couple of new quot
e
s
commit
|
commitdiff
|
tree
2016-11-18
Dav
i
d
van der S
p
oel
Added first tests of
b
onded
f
orce func
t
ions
.
commit
|
commitdiff
|
tree
2016-10-14
Da
v
id van
d
er Spoel
Fixes some
m
e
mo
r
y l
e
aks ass
o
ciated
wit
h
testi
n
g applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David va
n
der Sp
o
el
Modularize electr
i
c fiel
d
handling
commit
|
commitdiff
|
tree
2016-09-27
David
v
an der Sp
o
el
Fixed script xplor2gmx
.
p
l to work with GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David van der Spoel
Fixes issue w
i
th Release buil
d
in c
o
r
re
l
ation functions
.
commit
|
commitdiff
|
tree
2016-09-20
David
van der Spoel
M
a
d
e
correlation function
r
outine use s
t
d::vector
commit
|
commitdiff
|
tree
2016-09-05
David van de
r
Spoel
Merge
"
Mer
g
e
branch release-201
6
"
commit
|
commitdiff
|
tree
2016-08-24
David van der Spoel
Added d
o
cume
n
tation for shell pote
n
tials
.
commit
|
commitdiff
|
tree
2016-08-03
Da
v
id van de
r
S
poe
l
Th
r
ee new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David van der Spoel
M
e
rge "Merge br
a
nch releas
e
-5-1
i
nt
o
rel
e
a
s
e-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van der Spoel
Fixes incorrect charges
in OPLS/AA-L for
H
ISD and
HISE
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van der Spo
e
l
M
e
rge "Merge
b
ranch r
e
lease-5-1 into r
e
lease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Dav
i
d v
a
n
d
e
r
Spoel
Introdu
c
e f
a
t
a
l
e
r
r
or f
o
r too few fra
m
es in g
m
x dos
.
commit
|
commitdiff
|
tree
2016-06-27
David
van
der Spoel
M
a
d
e
g
mx d
o
s work again
.
commit
|
commitdiff
|
tree
2016-06-22
David van der Sp
o
e
l
R
e
moved
s
purious r_ij
i
n force for
Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David
v
an
der Sp
o
el
Modify
lmfit library to
a
void c
l
a
shes wi
t
h other v
e
rsi
o
n
s
.
commit
|
commitdiff
|
tree
2016-03-23
David van
d
er Spoel
R
e
moved
s
renew
that wa
s
m
aking array small
e
r
incor
r
ectly
.
commit
|
commitdiff
|
tree
2016-03-18
D
avid van der Spoe
l
Fixed
d
ivision by
z
ero in po
l
ariz
e
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Sp
o
el
Couple o
f
new quo
t
es
commit
|
commitdiff
|
tree
2016-01-07
Davi
d
van
d
er S
p
oel
Ma
d
e n
o
rmal modes work
w
i
t
h she
l
ls and vs
i
tes
commit
|
commitdiff
|
tree
2015-11-24
D
a
v
i
d v
a
n
d
e
r
Spoel
Fixes
n
ewly intro
d
uced bug in
make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David
v
an der
S
poel
Moved
d
omdec struc
t
ur
e
s ou
t
of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Dav
i
d va
n
d
er Sp
o
el
C
l
eanups in legacy
h
eader/
t
ypes/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
id van der Sp
o
el
M
erg
e
d
l
ega
c
yheaders/types/qmm
m
rec
.
h
into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
id van der Spoel
M
e
rged genborn
.
h fro
m
legacyheader
s
/
types into
m
dli
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
oel
Move
d
legac
y
headers/types/group
.
h
t
o mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
Sp
o
el
Mer
g
ed legacyheaders/types/ns
.
h and nb
l
ist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van der Spoel
Combine enums
.
h and names
*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Merged
l
egac
y
headers/
n
rn
b
.
h and ty
p
es
/
nrnb
.
h
to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der Spoel
Moved m
d
atom
.
h
f
ro
m
legacyheader/ty
p
es to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
der Spoel
Moved legac
y
h
e
a
ders/types/ene
r
gy
.
h to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-15
Da
v
id van der Spoel
Merged legacyh
e
aders/types/inputrec
.
h into mdtype
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David va
n
d
e
r Sp
o
el
Merged legacyheaders/type
s
/state
.
h into mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
D
avid van
d
er Spoel
Repl
a
ce
d
a
t
om_
i
d by int
.
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Moved genbor
n
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van
d
er Spoel
M
o
v
e
d t
x
tdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
av
i
d van d
e
r Spoel
Mo
v
ed copyrite
.
* to fil
e
io from gm
x
l
i
b
an
d
le
g
acyheade
r
s
.
commit
|
commitdiff
|
tree
2015-11-11
Davi
d
van der Spoel
M
o
ved inpu
t
re
c
.
* fro
m
gm
x
lib and legacyheaders
to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David
van der
S
poel
Remov
e
d legacyhe
a
ders/typed
e
f
s
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van de
r
Spoel
Moved d
f
_hi
s
t
ory
u
tility routines from typed
e
fs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
D
avid
van
der
S
p
o
el
Replaced NOTSET f
r
om ty
p
e
d
efs
.
h by
loca
l
soluti
o
n
s
.
commit
|
commitdiff
|
tree
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