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Version 2016.4
2017-08-15
David
van der Spoel
Worked aroun
d
missing Op
e
nMP implementation in orires
.
commit
|
commitdiff
|
tree
2017-03-04
Da
v
id v
a
n der Spo
e
l
Remo
v
es rogue
p
rinting to xvg file in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoel
F
ixes bug
i
n gmx solvate
w
ith -shell tha
t
yie
l
ded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David
v
an der Spoel
Fixe
s
SEGV in gmx
order
.
commit
|
commitdiff
|
tree
2016-09-27
David van der Spoel
Fixed
s
c
ript
x
plor2g
m
x
.
pl to work with GMXDATA
commit
|
commitdiff
|
tree
2016-08-03
Davi
d
van
d
er Spo
e
l
Thre
e
new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
Da
v
i
d va
n
der Spoel
Me
r
g
e
"Me
r
ge branch release-5-1
into
r
e
lease
-
2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David
v
an
d
er Spoel
Fixes incorr
e
ct charges
i
n OPLS
/
AA-L
for
HISD
a
n
d HI
S
E
commit
|
commitdiff
|
tree
2016-07-08
David va
n
d
e
r Spoel
Merge "Merge
b
r
a
nch relea
s
e-5
-
1 into r
e
lease-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van der S
p
oe
l
Introduc
e
f
atal error for t
o
o few fra
m
es
i
n gm
x
dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van de
r
Spoel
Made gmx dos w
o
rk
a
gain
.
commit
|
commitdiff
|
tree
2016-06-22
David van der Spoel
R
e
mo
v
e
d
spurious r_
i
j in
f
o
r
ce for Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van der
Spoel
Modify lmfit library t
o
avoid clashe
s
with ot
h
er versions
.
commit
|
commitdiff
|
tree
2016-03-23
Da
v
id van der Spoel
Removed sre
n
ew that was making a
r
ray sm
a
ller incorr
e
c
tly
.
commit
|
commitdiff
|
tree
2016-03-18
David
van
d
e
r S
p
o
el
Fixed
division by zero
i
n polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van
d
er S
p
oel
C
ou
p
le of
n
e
w quotes
commit
|
commitdiff
|
tree
2016-01-07
Dav
i
d van der Spoel
Ma
d
e normal
modes work
with she
l
ls
a
nd v
s
ites
commit
|
commitdiff
|
tree
2015-11-24
David
van d
e
r Spoe
l
Fixes newly introduced b
u
g in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der Spoel
Moved domdec structures out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David
v
an de
r
Spoel
Cleanups in legacyhe
a
der/ty
p
es/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
avid va
n
der
Spoel
M
erged legacyheaders/types/
q
mmmrec
.
h i
n
to mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van der Spoel
Mer
g
ed genborn
.
h f
r
om legacyheaders
/
t
y
pes in
t
o mdl
i
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid v
a
n de
r
Spoel
Moved
l
egacy
h
eaders/types
/
g
r
oup
.
h
t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spoel
Merged legacyheader
s
/t
y
pes/ns
.
h and nblist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spoel
Combine enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der S
p
oel
Merged le
g
acyheaders/
n
rnb
.
h and t
y
pe
s
/nrn
b
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
M
o
v
e
d mdatom
.
h from
l
egacyheader
/
types to mdtyp
e
s
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an
d
er Sp
o
el
Moved legacyheaders
/
type
s
/
energy
.
h t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Mer
g
ed le
g
a
cyheade
r
s/types/inputrec
.
h i
n
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van d
e
r S
p
oel
Merged legacyheaders/types/state
.
h into mdtypes/sta
t
e
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Replaced atom_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
David va
n
der Spoel
Mo
v
ed genborn
.
h
to mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
avid van der Spoel
Moved txtdump
.
*
to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
D
avid
v
a
n
der Spoel
Mo
v
ed
c
opyrite
.
* to fileio fr
o
m gmxlib and l
e
gacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
Da
v
id v
a
n de
r
Spoel
Moved i
n
putrec
.
*
f
r
o
m gmx
l
ib
and
l
eg
a
cyhe
a
ders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Removed leg
a
cyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der Spoel
Moved df_
h
istory utility r
o
utine
s
from
t
ypedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der Spoel
Replaced NOTSET fr
o
m type
d
efs
.
h by
l
ocal soluti
o
ns
.
commit
|
commitdiff
|
tree
2015-10-23
David van der Spoe
l
Removed en
e
r
g
y
history code from typedefs t
o
a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
Dav
i
d van der Spoel
M
o
ved pbc/cut-off
r
e
lat
e
d utilities fro
m
typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Fr
e
ed memor
y
in
l
egacy statist
i
cs rout
i
ne
s
.
commit
|
commitdiff
|
tree
2015-10-03
David van der
S
po
e
l
R
emoved
s
i
mple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David
van
d
er Sp
o
el
Rem
o
ved simple
.
h from
nb_ke
r
nel_sse4_1_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remov
e
d si
m
ple
.
h from
n
b_kernel_sse2_X
X
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid
v
an der Spoel
Removed s
i
mple
.
h
fr
o
m n
b
_
k
e
r
n
el_
c
and nb_kern
e
l_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
D
av
i
d van der Spoel
Remove
d
include simp
l
e
.
h from
n
b
_
k
e
rnel_avx_12
8
_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
mov
e
d simple
.
h from nb_ke
r
nel_avx
_
25
6
_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remov
e
d output_env_t, now us
i
n
g
gm
x
_outp
u
t_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Dav
i
d van de
r
Spoel
Removed types/nrnb
.
h f
r
o
m
t
y
pedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
D
avid van der Sp
o
el
R
e
mo
v
ed types/nblist
.
h and typ
e
s
/
nsgrid
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d van der Spo
e
l
Remov
e
d types/mdatom
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
R
e
moved types/inputrec
.
h fr
o
m typedefs
.
h a
n
d relete
d
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van de
r
Spoel
Fixes
bug
i
n
the computation of Coe
f
ficient of Therm
a
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
a
vi
d
van
d
e
r
S
p
o
el
Remo
v
e
d
ty
p
es/
f
or
c
erec
.
h fro
m
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
Da
v
id va
n
der Spoel
Remove
d
inc
l
ude
o
f
types/ifunc
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
avid va
n
der Spoel
Removed four
i
ncludes
f
r
o
m legacy
h
eaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Sp
o
el
Re
m
oved legacy
h
e
a
ders/types/
c
ommrec_fwd
.
h from ty
p
edef
.
h
commit
|
commitdiff
|
tree
2015-09-10
D
avid
v
an der
S
poel
Move
d
content from md
r
un
.
h to
se
p
a
rate headers
.
commit
|
commitdiff
|
tree
2015-09-10
Dav
i
d
van der Spoe
l
Rem
o
ved <s
y
s/t
y
pes
.
h> and "type
s
/cons
t
r
.
h" from typedef
s
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoel
Removed file
i
o/tr
x
.
h
fr
o
m
t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van der Sp
o
el
Moved functions op
e
rating on
for
c
erec
to sepa
r
ate header
.
commit
|
commitdiff
|
tree
2015-08-28
David van
d
e
r
Sp
o
e
l
Added
energy (
e
dr) file type to
Options he
a
ders
.
commit
|
commitdiff
|
tree
2015-08-28
David
van
der Spoel
Added additional const
r
uctor to StringStream class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
D
a
vid va
n
der Spoel
Mad
e
outp
u
t from
d
u
mping neight
b
o
r
lists
e
asie
r
to rea
d
.
commit
|
commitdiff
|
tree
2015-07-31
Dav
i
d van der
Spoel
Change initial parameters
f
or te
s
ting e
x
pfit
.
commit
|
commitdiff
|
tree
2015-07-29
D
a
vid van d
e
r Spoel
Code f
o
r
checking xvg files
in
testutils
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spoel
Updated exp
o
n
ential fitti
n
g t
o
m
ake i
t
rob
u
st
.
commit
|
commitdiff
|
tree
2015-04-09
Davi
d
v
an
der Spoel
C
l
arified commen
t
s for t
i
me-dependent electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
Dav
i
d van
d
e
r Spoel
Fixed
i
nco
r
r
e
ct output
of gb_a
l
gorith
a
s sa_algo
r
ith
m
.
commit
|
commitdiff
|
tree
2015-03-02
David van der
S
p
o
el
Updated document
a
tion for
electric fie
l
ds
.
commit
|
commitdiff
|
tree
2014-12-13
David van d
e
r
Spoel
Four new quotes
from ar
o
und
the world
.
commit
|
commitdiff
|
tree
2014-11-28
David van
der Spo
e
l
Fixes recently introduced b
u
g in gm
x
analyze
.
commit
|
commitdiff
|
tree
2014-11-24
Davi
d
van der Spoel
Added
warnings for ew
a
ld-geometry and surface-ep
s
ilon
commit
|
commitdiff
|
tree
2014-10-28
Davi
d
van der Spoel
Even mor
e
refreshing q
u
ote
s
.
commit
|
commitdiff
|
tree
2014-10-14
David va
n
der S
p
oel
Reorganiz
i
ng analysis of corr
e
lation fu
n
cti
o
n
s
.
commit
|
commitdiff
|
tree
2014-09-23
David
v
an der Spoe
l
Fixes potential bug in neighbo
r
sear
c
h
i
ng
.
commit
|
commitdiff
|
tree
2014-09-17
Da
v
id v
a
n
der S
p
oel
M
e
rge release-
5
-0 into master
commit
|
commitdiff
|
tree
2014-09-10
David van de
r
Spoe
l
Remove
.
tpa,
.
tpb,
.
tpx
,
.
trj
files
.
Part
o
f #150
0
.
commit
|
commitdiff
|
tree
2014-08-30
David van d
e
r Sp
o
el
Fixes is
s
ue wi
t
h
v
siten and
v
e
r
l
et
b
uffers
.
commit
|
commitdiff
|
tree
2014-07-05
Dav
i
d
van der Spoel
Fix
e
d
inconsistenc
y
in b
l
ocka handling
.
commit
|
commitdiff
|
tree
2014-06-29
D
avid van de
r
Spoel
Fixes #1532, SEGV in g_c
u
rrent
.
commit
|
commitdiff
|
tree
2014-06-25
D
a
vid van d
e
r Spo
e
l
Added check fo
r
domain decomposition and shells
.
commit
|
commitdiff
|
tree
2014-06-24
David van der Spoel
A
dded c
h
eck
in grom
p
p for shells
a
nd inputrec issues
.
commit
|
commitdiff
|
tree
2014-06-22
David van der Sp
o
e
l
I
m
plemented fata
l
e
r
ro
r
fo
r
n
s
tcal
c
energy!=1 with shells
.
commit
|
commitdiff
|
tree
2014-06-13
David va
n
d
e
r Spoel
Fi
x
memo
r
y-usag
e
error in g_chi
commit
|
commitdiff
|
tree
2014-06-11
Davi
d
van der Spoel
F
i
xe
s
bug w
h
ere -e and
-
dt
fla
g
s d
i
d not w
o
r
k an
y
m
ore
.
commit
|
commitdiff
|
tree
2014-06-07
David van
der Spoel
Me
r
g
e
"Merge release-5-0
in
t
o master"
commit
|
commitdiff
|
tree
2014-06-07
David van der Spoel
Merge rele
a
se-5-0 into mas
t
er
commit
|
commitdiff
|
tree
2014-06-02
D
avi
d
van der Spoel
Fixed wrong jo
u
rnal
re
f
ere
n
c
e in ma
n
ual
commit
|
commitdiff
|
tree
2014-05-31
Davi
d
v
a
n
der S
p
o
el
Permit trjconv to read and write velocities with TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David van der Spoel
Fixes
a com
p
licated b
u
g
in g_anaeig
.
commit
|
commitdiff
|
tree
2014-05-15
David va
n
d
e
r Spoel
Added cmake profil
i
ng support
commit
|
commitdiff
|
tree
2014-04-02
Dav
i
d van der Sp
o
el
Removed possibility of compiling
with
GSL
.
commit
|
commitdiff
|
tree
2014-03-31
Davi
d
van
d
er
S
p
o
e
l
Fixed compi
l
at
i
o
n issue in f
g
ri
d
.
cpp
d
ue to
int/enum
commit
|
commitdiff
|
tree
2014-03-06
David v
a
n der Spoel
Six new quotes fro
m
classic literature
.
commit
|
commitdiff
|
tree
2014-02-11
David van
d
er Spoe
l
Fixed
a
n
other vmdio
i
ssue
.
commit
|
commitdiff
|
tree
2014-02-10
D
avid
va
n
de
r
S
p
oel
M
o
v
ed
con
d
itional cmak
e
c
o
de for v
m
di
o
.
commit
|
commitdiff
|
tree
2014-01-28
David van der Spoel
Moved ran
d
om number gene
r
at
o
r code
t
o
separate dir
.
commit
|
commitdiff
|
tree
2014-01-18
Davi
d
van der Spoel
This patch moves the statisti
c
s lib
r
ary to its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
David van der Sp
o
e
l
This p
a
tch moves pre
p
roces
s
ing headers to gmxpreprocess
commit
|
commitdiff
|
tree
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