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Update instructions in containers.rst
2020-09-17
David v
a
n
d
er Spoe
l
Add relea
s
e
n
ote
s
commit
|
commitdiff
|
tree
2020-02-22
David van
der Spoel
Fix
e
d
bug in
gm
x
disre
d
u
e
to inconsistency in input
.
commit
|
commitdiff
|
tree
2020-02-20
David
va
n
der Spoel
Fixed bug
i
n ori
r
es
code that was checking to
o
s
tri
c
t
.
commit
|
commitdiff
|
tree
2020-02-20
Da
v
id van de
r
Spoel
Fixe
d
bug in orire
s
code
t
hat was chec
k
ing too strict
.
commit
|
commitdiff
|
tree
2020-02-18
Dav
i
d van der Spoel
Fixed t
y
po in GM
X
RC
.
csh
.
cmak
e
in
commit
|
commitdiff
|
tree
2019-07-09
David v
a
n der Spoel
Fixed sma
l
l bug in gmx anaei
g
commit
|
commitdiff
|
tree
2019-04-05
David van
d
er Sp
o
el
Fix
e
d m
a
n
u
a
l
for
dihedral re
s
traints
.
commit
|
commitdiff
|
tree
2019-03-31
David
van der Spoel
R
emo
v
ed confusi
n
g
g
p
p_
a
tomtype functio
n
s
.
commit
|
commitdiff
|
tree
2019-02-18
David van der Spoel
Precision fix
f
o
r
rescbt
code
.
commit
|
commitdiff
|
tree
2019-02-16
David v
a
n der Spoel
Tests of res
t
r
a
i
ned
l
isted pote
n
tials
.
commit
|
commitdiff
|
tree
2019-02-11
David
van
d
er Spoel
Remove buggy de
b
ug output
.
commit
|
commitdiff
|
tree
2019-02-11
David
van der Spoe
l
Tests fo
r
polariz
a
tion
functi
o
ns
.
commit
|
commitdiff
|
tree
2019-02-08
D
a
vid
v
an
der Spoel
F
urther increa
s
e of
t
oleranc
e
for angle
s
.
commit
|
commitdiff
|
tree
2019-02-08
D
avid v
a
n der S
p
oel
Increased to
l
erance for angl
e
functions
.
commit
|
commitdiff
|
tree
2019-02-08
Dav
i
d
v
an der Spoel
Increase tolerance in Angle test
.
commit
|
commitdiff
|
tree
2019-02-08
David van der Spoel
Test
s
for l
i
sted force
p
ote
n
tia
l
s
.
commit
|
commitdiff
|
tree
2019-01-26
David
v
an der Spoel
F
ixed some typos in com
m
en
t
s
.
commit
|
commitdiff
|
tree
2019-01-17
David
van der Spoel
Allow multiple
co
o
rdina
t
e sets in liste
d
_
f
or
c
es test
.
commit
|
commitdiff
|
tree
2019-01-17
David van der Spoel
Mov
e
d
one regre
s
siontest to core gromacs
.
commit
|
commitdiff
|
tree
2019-01-14
David van
d
e
r
Spoel
MSD tests for the -mol option
.
commit
|
commitdiff
|
tree
2019-01-11
D
avid v
a
n der Spoel
Added low
-
le
v
el tests for improper di
h
edrals
.
commit
|
commitdiff
|
tree
2018-12-31
David van
d
er Spoel
Moved generic
s
imul
a
ti
o
ndatabase code to
testuti
l
s
.
commit
|
commitdiff
|
tree
2018-12-30
David v
a
n
d
e
r Spoel
Move
d
input
f
ile
s
for
t
ests to
simul
a
ti
o
n database
.
commit
|
commitdiff
|
tree
2018-12-30
David van der
S
p
oel
Implemented nati
v
e
n
o
r
mal mo
d
e analysis tests
.
commit
|
commitdiff
|
tree
2018-12-22
D
a
vid van der S
p
o
el
Rever
t
"Removed t_topology from gmx msd"
commit
|
commitdiff
|
tree
2018-12-20
David van der Spo
e
l
Rem
o
ved t_
t
opol
o
gy fro
m
gmx msd
commit
|
commitdiff
|
tree
2018-12-05
David van
d
e
r
S
p
oe
l
Add
e
d
new te
s
ti
n
g code for normal
m
o
de analysis
.
commit
|
commitdiff
|
tree
2018-12-04
David van
der Spoel
Small
update to mdrun t
e
sts
.
commit
|
commitdiff
|
tree
2018-12-04
David van d
e
r Spoe
l
Removed
g
mx morph
commit
|
commitdiff
|
tree
2018-12-04
Davi
d
van der Spoel
Removed gmx dyndom
commit
|
commitdiff
|
tree
2018-12-04
D
avid van der Spoel
Remov
e
d
g
mx anado
c
k
commit
|
commitdiff
|
tree
2018-11-21
David
v
an der Sp
o
el
Merge branch 'rele
a
se-
2
0
1
9'
commit
|
commitdiff
|
tree
2018-11-18
David van der Spoel
Added citation for new
a
naly
s
is functionality
.
commit
|
commitdiff
|
tree
2018-11-11
David v
a
n der Sp
o
el
F
ix en
t
ro
p
y calculation in gmx
an
a
eig
commit
|
commitdiff
|
tree
2018-11-09
David van der Spoel
Ch
a
nge get
_
a
tom_
i
nde
x
to allow mu
l
tiple molecule
s
.
commit
|
commitdiff
|
tree
2018-10-11
D
avid van
d
e
r Spoel
Reinstated q
u
asiharmonic entrop
y
c
alculati
o
n
i
n gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
D
avid van der Spoel
Add
e
d
opt
i
o
n
to gmx nmeig
to print ZPE
.
commit
|
commitdiff
|
tree
2018-06-12
David
v
a
n d
e
r
S
po
e
l
Let
gmx nmeig pr
i
n
t
thermoc
h
emis
t
ry
.
commit
|
commitdiff
|
tree
2018-03-21
David van der Spoel
Renamed entrop
y
.
* to t
h
er
m
oche
m
istry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van
der Spoel
Split off entr
o
py calculation
to
separa
t
e
f
ile
.
commit
|
commitdiff
|
tree
2017-12-28
Da
v
id van der Spoel
Fix
e
s
and updates for xplor
2
g
m
l
.
pl and atom_no
m
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van
d
er
Spoel
Fixed check for
w
a
ter in gen_vsi
t
e
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David va
n
der
S
poel
New
m
dp i
n
put fo
r
electric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
Fixed mdp output
f
rom elec
t
ric field code
.
commit
|
commitdiff
|
tree
2017-10-30
D
avid van der Spoel
Added opt
i
on -wat
e
r
tips3p to
p
db2g
m
x
.
commit
|
commitdiff
|
tree
2017-10-23
Dav
i
d van
der
S
poel
Split
off the NMR related
a
nal
y
ses from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
Da
v
id van der S
p
o
e
l
Fixe
d
m
i
s
s
ing entries in nr
n
b arrays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoel
W
orked
a
r
o
und mi
s
sing OpenMP i
m
plemen
t
ation
i
n
ori
r
es
.
commit
|
commitdiff
|
tree
2017-08-03
D
a
v
id van der
Spoel
Fixe
d
bug in gm
x
d
isres indexing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
Da
v
id van der Spoel
Worke
d
around
missing OpenMP imp
l
ementatio
n
in
o
rires
.
commit
|
commitdiff
|
tree
2017-07-28
David
v
an
d
er Spoel
Added unit
-
test for or
i
e
n
ta
t
ion restraints output
.
commit
|
commitdiff
|
tree
2017-07-19
Dav
i
d van der Spoel
Remov
e
d unnecess
a
r
y
static de
c
l
a
rations for com
m
and
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
D
avid
v
a
n der Spo
e
l
Fixed test-order d
e
pend
e
ncy
in gmxpreproc
e
ss tests
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid van der Spoel
Fix non-reproduc
a
bili
t
y
of clustsize
tests
.
commit
|
commitdiff
|
tree
2017-05-01
Dav
i
d v
a
n
der S
p
oel
X
pm t
e
st for gmx clustsize
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoel
A
dded tests fo
r
gmx
clustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David van der Spoel
Removes
r
ogue printi
n
g to x
v
g file in gmx mind
i
st
commit
|
commitdiff
|
tree
2017-02-27
D
a
vid va
n
d
er Spoe
l
Fixes bu
g
in
gmx solvate
w
ith -s
h
ell
t
h
at yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
D
a
vid van der
Spoel
Fi
x
e
s
SEGV in gmx
o
rder
.
commit
|
commitdiff
|
tree
2017-02-02
David va
n
der Spoel
Only pri
n
t all dang
l
i
n
g atoms w
i
th gr
o
m
pp -v
commit
|
commitdiff
|
tree
2017-01-23
David
van
d
er Spoel
Added refe
r
ence for dihed
r
al
functio
n
in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der
S
poel
Couple
of new quotes
commit
|
commitdiff
|
tree
2016-11-18
David van de
r
Spoel
Added fir
s
t tests of b
o
nded f
o
rce functions
.
commit
|
commitdiff
|
tree
2016-10-14
D
avid
van
d
er Spoe
l
Fixes
s
ome
m
e
mory
l
eaks associa
t
ed with
t
esting applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David v
a
n der Spoel
Modularize ele
c
tric field handling
commit
|
commitdiff
|
tree
2016-09-27
D
avid va
n
der Spoel
Fixed script xp
l
or2g
m
x
.
p
l t
o
work
w
i
th GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David van
der Sp
o
el
Fixes issue w
i
th Relea
s
e
b
u
ild in correlation function
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van
d
er Spoel
Made correlation function routine use std::v
e
ctor
commit
|
commitdiff
|
tree
2016-09-05
Davi
d
van der Sp
o
el
Merge
"
M
erge b
r
an
c
h release-2016"
commit
|
commitdiff
|
tree
2016-08-24
Dav
i
d
van der
Spoe
l
Ad
d
ed
d
ocume
n
tation for shell po
t
entials
.
commit
|
commitdiff
|
tree
2016-08-03
Da
v
id van der S
p
o
e
l
Three new qu
o
tes
.
commit
|
commitdiff
|
tree
2016-07-31
D
avid
van der Spoel
Me
r
ge "Me
r
ge branch rele
a
se-5-1 into r
e
lease-
2
016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
D
avid van
de
r
Spoel
Fix
e
s
i
ncor
r
ect
charg
e
s in OPLS/AA-L
f
or H
I
S
D
and HISE
commit
|
commitdiff
|
tree
2016-07-08
Davi
d
van der Spoel
Merge "Mer
g
e
b
ranc
h
r
ele
a
se-5-1 into release
-
2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
Int
r
o
d
uc
e
fatal er
r
or for too few frames in gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made
g
mx dos wor
k
again
.
commit
|
commitdiff
|
tree
2016-06-22
David van der
S
po
e
l
Removed spurious r
_
ij i
n
forc
e
for Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Dav
i
d v
a
n der Spoel
M
o
dify
lmfit
library to avoid clashes with ot
h
er
v
ersi
o
ns
.
commit
|
commitdiff
|
tree
2016-03-23
D
a
vi
d
van der Spoel
Removed srenew that
w
as making a
r
r
ay
smaller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
D
avid va
n
der Spoel
Fixed division by zero
i
n p
o
l
arize
.
commit
|
commitdiff
|
tree
2016-01-20
D
a
vid van
de
r
Spoel
Couple of
n
e
w qu
o
tes
commit
|
commitdiff
|
tree
2016-01-07
David van der Sp
o
el
Made nor
m
a
l modes wo
r
k
with shells
a
nd vsites
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
Fixe
s
newly intro
d
u
c
e
d
bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
D
a
v
i
d
van der Spoel
M
o
ved domdec st
r
uc
t
u
r
e
s out of
c
ommre
c
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Dav
i
d va
n
der Spoe
l
Cleanu
p
s in lega
c
yh
e
a
d
er/t
y
p
e
s/co
m
mrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
v
an der
Spoel
M
e
r
ged l
e
gacyhe
a
ders/types/qmmm
r
ec
.
h into mdlib/
q
mmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van der Sp
o
el
Mer
g
e
d
g
enborn
.
h from legacyheaders/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved legacy
h
eaders/types/grou
p
.
h to m
d
ty
p
es
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der Sp
o
el
Me
r
ged le
g
acyheade
r
s/types/ns
.
h
a
n
d
nbl
i
st
.
h to mdtyp
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Combine enums
.
h and nam
e
s*
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er Spo
e
l
M
e
rged legacyheaders/nrnb
.
h and types/nrnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David v
a
n der Spoe
l
Moved mdat
o
m
.
h from legac
y
header/types
t
o mdt
y
pe
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er Spoel
Moved l
e
g
a
cyhea
d
e
r
s/types/energ
y
.
h to
m
dtypes
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid v
a
n der Spoel
Merged legacy
h
e
aders/t
y
pes/inpu
t
re
c
.
h
into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Da
v
id van der Spoel
Merge
d
lega
c
yheade
r
s/types/st
a
te
.
h
into mdtyp
e
s/sta
t
e
.
h
commit
|
commitdiff
|
tree
2015-11-13
Davi
d
van der Spoel
Re
p
laced at
o
m_id
by in
t
.
commit
|
commitdiff
|
tree
2015-11-13
David van d
e
r Sp
o
el
M
oved ge
n
born
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
Dav
i
d van der Spoe
l
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
avid van d
e
r Spoel
Moved co
p
yr
i
te
.
*
to fileio fro
m
gmxlib and legacyhea
d
ers
.
commit
|
commitdiff
|
tree
2015-11-11
David van
d
e
r
S
p
oel
Moved inpu
t
rec
.
*
from gmxlib a
n
d
legacyh
e
aders to
m
d
t
y
pes
.
commit
|
commitdiff
|
tree
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