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Update instructions in containers.rst
2020-09-17
David van der Spoel
Add releas
e
notes
commit
|
commitdiff
|
tree
2020-02-22
David van der Spoel
Fix
e
d bug
i
n gmx d
i
sre due to i
n
consistency in
input
.
commit
|
commitdiff
|
tree
2020-02-20
Dav
i
d van
der Spoel
Fixe
d
b
ug in orires code that was ch
e
c
king
t
o
o
s
t
rict
.
commit
|
commitdiff
|
tree
2020-02-20
David van der S
p
oel
Fixed
bug i
n
orires code that was
c
hecking too strict
.
commit
|
commitdiff
|
tree
2020-02-18
Davi
d
van der Spoel
F
i
x
e
d ty
p
o in GMXRC
.
csh
.
cmakein
commit
|
commitdiff
|
tree
2019-07-09
D
a
vid
v
an der Spo
e
l
F
ixed small bug i
n
gmx anaeig
commit
|
commitdiff
|
tree
2019-04-05
D
avi
d
van de
r
Spoel
Fixed
manual for
d
ihedral restraints
.
commit
|
commitdiff
|
tree
2019-03-31
David v
a
n
d
er Spoel
Remo
v
ed confusing
gpp_a
t
omtyp
e
functions
.
commit
|
commitdiff
|
tree
2019-02-18
David van der Spoel
Precision fix for rescbt code
.
commit
|
commitdiff
|
tree
2019-02-16
D
a
vid va
n
der Spoel
Test
s
of restrained listed
p
otentials
.
commit
|
commitdiff
|
tree
2019-02-11
D
a
vid van de
r
Spo
e
l
Rem
o
ve bu
g
gy debu
g
output
.
commit
|
commitdiff
|
tree
2019-02-11
Da
v
id van
der S
p
oel
Tes
t
s
for polarization functions
.
commit
|
commitdiff
|
tree
2019-02-08
David
va
n
d
e
r
S
p
oel
F
urther
increase
of tolerance
for angles
.
commit
|
commitdiff
|
tree
2019-02-08
David
v
an der Spo
e
l
Increased tol
e
ranc
e
for angle func
t
ion
s
.
commit
|
commitdiff
|
tree
2019-02-08
Davi
d
van d
e
r
S
poel
Increase t
o
l
e
ran
c
e in
Angle
te
s
t
.
commit
|
commitdiff
|
tree
2019-02-08
Da
v
id
van der Spoel
Tests for listed f
o
r
ce potentials
.
commit
|
commitdiff
|
tree
2019-01-26
David van der Spoel
Fixed some typos in
c
om
m
en
t
s
.
commit
|
commitdiff
|
tree
2019-01-17
David van der Spoel
A
ll
o
w mul
t
iple coor
d
inate
sets in l
i
sted_f
o
rce
s
test
.
commit
|
commitdiff
|
tree
2019-01-17
D
a
vi
d
v
an der Spoel
Moved one re
g
r
ess
i
o
ntest t
o
c
ore g
r
omacs
.
commit
|
commitdiff
|
tree
2019-01-14
Davi
d
van
der Spoel
MSD
tests for the -mol opt
i
on
.
commit
|
commitdiff
|
tree
2019-01-11
David van der Spoel
Added low-level tests for improper dihedrals
.
commit
|
commitdiff
|
tree
2018-12-31
Dav
i
d van der
Sp
o
e
l
Moved generic simula
t
iondatabase code to
t
estutils
.
commit
|
commitdiff
|
tree
2018-12-30
Da
v
id van
d
er Spoe
l
Moved inp
u
t fil
e
s
for tests to
s
imulation database
.
commit
|
commitdiff
|
tree
2018-12-30
David van der Spoel
I
m
ple
m
ented native norma
l
mode anal
y
sis tests
.
commit
|
commitdiff
|
tree
2018-12-22
Da
v
id
v
an der
S
poe
l
R
e
vert "
R
emoved t_topology from
g
m
x msd"
commit
|
commitdiff
|
tree
2018-12-20
D
av
i
d van
d
e
r
Sp
o
el
Remove
d
t_topology
f
r
om gm
x
ms
d
commit
|
commitdiff
|
tree
2018-12-05
Dav
i
d
van
der Spoel
Add
e
d new testing code for normal
m
ode
analysis
.
commit
|
commitdiff
|
tree
2018-12-04
D
a
vid van der S
p
oel
Small update t
o
mdrun tes
t
s
.
commit
|
commitdiff
|
tree
2018-12-04
David van
d
e
r Spoel
Removed
gm
x
mo
r
ph
commit
|
commitdiff
|
tree
2018-12-04
David van d
e
r Spoe
l
Removed gm
x
d
y
ndom
commit
|
commitdiff
|
tree
2018-12-04
Dav
i
d
v
an der
Spoel
Removed gmx ana
d
ock
commit
|
commitdiff
|
tree
2018-11-21
Dav
i
d va
n
der
Spoel
Merge bran
c
h 'release-2
0
19'
commit
|
commitdiff
|
tree
2018-11-18
D
a
v
id
v
an der Sp
o
el
Adde
d
citation for new
analysis functi
o
nality
.
commit
|
commitdiff
|
tree
2018-11-11
David van der Spoel
Fix
e
ntropy calculati
o
n
in gmx anaeig
commit
|
commitdiff
|
tree
2018-11-09
Dav
i
d van der Spoel
Change get_atom_index to allow mult
i
ple molecules
.
commit
|
commitdiff
|
tree
2018-10-11
David van de
r
Spo
e
l
Rein
s
tat
e
d qua
s
iharmonic entropy calculation in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
D
a
vid
v
an der Spoel
Added option to gmx
nmeig to print Z
P
E
.
commit
|
commitdiff
|
tree
2018-06-12
David van de
r
Spoel
Let gmx nmeig
print thermochemis
t
ry
.
commit
|
commitdiff
|
tree
2018-03-21
D
avid van d
e
r
S
poel
Renam
e
d entropy
.
* to thermoch
e
mistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David va
n
d
e
r Spoel
Split off entro
p
y ca
l
culation
to separate fi
l
e
.
commit
|
commitdiff
|
tree
2017-12-28
David va
n
d
er Spoel
Fixes
and updates for xplor2g
m
l
.
p
l
and at
o
m_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van der Spoel
Fix
e
d ch
e
c
k
fo
r
water in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David va
n
de
r
S
poel
New m
d
p input for
e
lectric
fields
.
commit
|
commitdiff
|
tree
2017-10-30
Da
v
i
d
van der Spoel
Fixed mdp output f
r
om ele
c
tric field
code
.
commit
|
commitdiff
|
tree
2017-10-30
Da
v
id van d
e
r Spoel
Added opt
i
o
n -water tips3p to pdb2g
m
x
.
commit
|
commitdiff
|
tree
2017-10-23
Dav
i
d van
d
er Spoel
Split off the NMR rel
a
ted a
n
a
lyses from
g
mx energy
.
commit
|
commitdiff
|
tree
2017-10-17
D
avid
van d
e
r Sp
o
el
Fixed missing entries in nrnb
arrays
.
commit
|
commitdiff
|
tree
2017-08-15
David van
d
er
Spo
e
l
W
o
rked around missing Op
e
nMP implementation in or
i
res
.
commit
|
commitdiff
|
tree
2017-08-03
David van der Spo
e
l
F
ixed bu
g
i
n gmx disres inde
x
ing a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-02
David van der
S
poel
Worked
a
round missin
g
O
penMP imp
l
ementa
t
ion in orires
.
commit
|
commitdiff
|
tree
2017-07-28
Da
v
id van
d
er Spoel
A
d
ded
u
nit-test for orientati
o
n
re
s
t
ra
i
nts outp
u
t
.
commit
|
commitdiff
|
tree
2017-07-19
D
avi
d
van d
e
r Spo
e
l
Remove
d
unn
e
cessary static declaration
s
for
c
ommand
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David
van der Spoel
Fixe
d
test-
o
rde
r
d
e
p
endency in
g
mx
p
reprocess test
s
.
commit
|
commitdiff
|
tree
2017-07-19
David van
d
e
r
S
poe
l
Fi
x
non-repr
o
du
c
a
bility
of clusts
i
z
e
tests
.
commit
|
commitdiff
|
tree
2017-05-01
David van der Spoel
Xpm test for gmx clus
t
size
commit
|
commitdiff
|
tree
2017-03-12
Davi
d
van der
Spo
e
l
A
dde
d
tes
t
s for gmx clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David va
n
de
r
Spoel
Removes rogue
printing
t
o
xvg
f
ile in gm
x
m
i
n
dis
t
commit
|
commitdiff
|
tree
2017-02-27
David van der
S
poel
Fixes bug in gmx solv
a
te with -shell
that yiel
d
ed
0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van der Spoel
Fi
x
es
S
EGV in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
David van der
S
p
o
e
l
Only print all dangling atoms with grompp
-
v
commit
|
commitdiff
|
tree
2017-01-23
David va
n
d
e
r Spoel
Added reference
for dihedra
l
function in OP
L
S
.
commit
|
commitdiff
|
tree
2016-12-07
Dav
i
d van der
S
poe
l
Couple
o
f new quo
t
es
commit
|
commitdiff
|
tree
2016-11-18
David va
n
der Spoel
Added first tests o
f
bonded force fun
c
tions
.
commit
|
commitdiff
|
tree
2016-10-14
David van der Spoel
F
ixe
s
some memory leaks assoc
i
ated wi
t
h te
s
t
i
ng applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van der Spoel
M
o
du
l
arize e
l
ectric fiel
d
hand
l
i
ng
commit
|
commitdiff
|
tree
2016-09-27
David van de
r
Spoe
l
Fi
x
ed script
x
plor2gm
x
.
pl to
work w
i
th
GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David
van der Spoel
Fix
e
s issue with
Rel
e
ase build in correlation fu
n
ction
s
.
commit
|
commitdiff
|
tree
2016-09-20
David
va
n
der
Spoel
Made correl
a
ti
o
n function
r
outine use std::vect
o
r
commit
|
commitdiff
|
tree
2016-09-05
Dav
i
d van der Sp
o
el
Merge "Merge branch r
e
l
e
ase-
2
016"
commit
|
commitdiff
|
tree
2016-08-24
David va
n
d
e
r Spoel
Added
d
ocumentatio
n
f
o
r shell p
o
t
e
ntials
.
commit
|
commitdiff
|
tree
2016-08-03
David van der Spoel
Thr
e
e new
q
u
otes
.
commit
|
commitdiff
|
tree
2016-07-31
David van der S
p
oel
Merg
e
"Merge
branch release-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
Davi
d
v
an der Spoel
Fix
e
s
incorrect
charges in OPLS
/
A
A-L for HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
David van der Sp
o
el
Me
r
ge "Me
r
ge branch release-5-
1
into re
l
e
ase-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David
van der
Spoel
Introduce f
a
tal err
o
r for
t
o
o
few frames i
n
g
m
x dos
.
commit
|
commitdiff
|
tree
2016-06-27
Da
v
id van der
Spoel
Ma
d
e gm
x
dos work again
.
commit
|
commitdiff
|
tree
2016-06-22
D
avid van der Spo
e
l
Removed spurious r_ij in f
o
r
c
e for Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
D
avi
d
van der Spoe
l
Modify lmfit
library to a
v
oid
clashe
s
with other
v
ers
i
o
ns
.
commit
|
commitdiff
|
tree
2016-03-23
David van der
S
p
o
el
Rem
o
ved sre
n
ew that
w
as makin
g
array smaller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der Spoel
Fixed div
i
sion by
z
ero
in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
D
a
vi
d
van der Spoel
Coup
l
e
of
n
ew quotes
commit
|
commitdiff
|
tree
2016-01-07
David v
a
n der Spoe
l
Made nor
m
a
l
mode
s
w
o
rk with
she
l
l
s
a
n
d vsite
s
commit
|
commitdiff
|
tree
2015-11-24
David van
d
er Spoel
Fixes newl
y
introduced bug
i
n make_nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
Davi
d
van de
r
Spoel
Moved dom
d
ec stru
c
tu
r
es out of c
o
m
mrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Da
v
id van der Spoel
C
l
ea
n
ups
i
n
lega
c
yh
e
ader/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Sp
o
el
Merge
d
legacyhea
d
ers/types/qmmmre
c
.
h
into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van der Spoel
Merg
e
d genborn
.
h from legacyheaders/t
y
pes into mdli
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
av
i
d van der Spoel
Moved legacyhea
d
ers/
t
ypes/group
.
h
to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spo
e
l
Merged legacyheaders/ty
p
es/ns
.
h an
d
nblist
.
h to m
d
types
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Combine
e
n
ums
.
h
a
nd names*
.
commit
|
commitdiff
|
tree
2015-11-20
David va
n
de
r
Spoel
Merged
legacyheader
s
/nrnb
.
h and
t
ypes/nrnb
.
h to gm
x
lib
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid
v
an
d
e
r
Spo
e
l
Mov
e
d
mdatom
.
h fro
m
l
e
gacyheader/types to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der
S
po
e
l
Moved
l
eg
a
cyheaders/ty
p
es
/
energy
.
h
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der
S
poel
Merg
e
d
legacyheaders/ty
p
es/inputr
e
c
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van der Spoel
Merged legacyheaders/types
/
s
tate
.
h into
m
dtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d van
d
er Spoe
l
Re
p
laced
atom_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
David
v
a
n der Spoel
Moved ge
n
born
.
h t
o
mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
avid van der Sp
o
el
M
o
ved txt
d
ump
.
* t
o
fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der
S
poel
Moved copyrite
.
*
to fileio from gmxl
i
b
a
nd
legacyheader
s
.
commit
|
commitdiff
|
tree
2015-11-11
Davi
d
v
a
n der
Spoel
M
o
ved inp
u
trec
.
* from gmxlib and legacyheaders to mdtypes
.
commit
|
commitdiff
|
tree
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