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Added pull potential flat-bottom-high
2016-01-20
David van
de
r
Spoel
Couple o
f
new quotes
commit
|
commitdiff
|
tree
2016-01-07
David
v
a
n
der Spoel
M
ade normal modes
work with shells and vsite
s
commit
|
commitdiff
|
tree
2015-11-24
David van
de
r
S
poel
Fixes newly introduc
e
d bug in make_nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
David van
d
er Spoel
M
o
v
e
d domdec
stru
c
t
u
res out of com
m
rec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Da
v
id van
der Spoel
Cleanup
s
in
l
ega
c
y
h
eader/types/comm
r
ec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
v
an der S
p
o
e
l
Merged legacyheaders/types/qmmmrec
.
h into mdlib/
q
m
mm
.
h
commit
|
commitdiff
|
tree
2015-11-21
Da
v
id van der
S
poel
M
e
rged genborn
.
h
from legacy
h
eaders/type
s
i
n
to
m
dlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vi
d
va
n
der
Sp
o
el
Moved legacyheader
s
/types/group
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der
Sp
o
el
M
e
r
g
ed
legacyh
e
ader
s
/types/ns
.
h and nblist
.
h to mdt
y
pe
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
C
ombine enums
.
h and name
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
v
id van de
r
S
p
oel
M
e
rged
l
eg
a
cyh
e
a
ders/nrnb
.
h and types/nr
n
b
.
h to gmx
l
ib
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
i
d va
n
d
e
r Spoel
Moved mdatom
.
h from legacyheader
/
t
y
pes to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r Spo
e
l
Moved legacyheaders/
t
ypes/energy
.
h to mdt
y
p
e
s
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van der Sp
o
el
Merged legacyheaders/typ
e
s
/
inp
u
tre
c
.
h
into
m
dtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David va
n
der Spoel
M
erged legacyheaders/type
s
/state
.
h into mdtype
s
/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d
van der S
p
oel
Re
p
laced atom_id by
int
.
commit
|
commitdiff
|
tree
2015-11-13
D
a
v
i
d van der
Spo
e
l
M
oved genborn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
Davi
d
van de
r
S
p
oel
Moved
txtd
u
mp
.
* to fil
e
io
.
commit
|
commitdiff
|
tree
2015-11-12
Dav
i
d v
a
n der
S
poel
M
o
ved copyrite
.
*
to
fi
l
eio from
g
mxlib and legacyheade
r
s
.
commit
|
commitdiff
|
tree
2015-11-11
David van der
S
p
oel
M
o
ved inputrec
.
* from
g
mxlib and leg
a
c
yheaders to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van der S
p
oel
R
e
move
d
legacyh
e
aders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
D
avid van der Spoel
Moved df_history utility routi
n
es fr
o
m typedefs
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Da
v
id van der S
p
oel
Rep
l
a
ced NOTSET from
typedefs
.
h by local solutions
.
commit
|
commitdiff
|
tree
2015-10-23
Davi
d
van der
S
poel
Remo
v
ed energy
h
i
stor
y
code fr
o
m
t
ypedefs to
a
s
eparate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van
der Spoel
M
oved pbc/c
u
t-off rela
t
ed utilities
from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van d
e
r Spoel
F
reed m
e
mory
in legacy statist
i
cs rout
i
nes
.
commit
|
commitdiff
|
tree
2015-10-03
David
van
d
er Spo
e
l
Remo
v
ed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spo
e
l
Removed
simple
.
h from
nb_
k
erne
l
_
sse
4
_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der
S
poel
R
e
moved sim
p
le
.
h fr
o
m
n
b_k
e
rnel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vid van d
e
r Spoel
Removed simple
.
h
from nb_kernel_c an
d
nb_kern
e
l_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van
der Spo
e
l
Remove
d
include s
i
mple
.
h from nb_kernel_avx_128_fm
a
_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed s
i
mpl
e
.
h
f
r
o
m
n
b_k
e
rnel_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van
d
er
S
poel
Removed output_env_t, now
u
sing gm
x
_outpu
t
_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Davi
d
van der Spoel
Remove
d
ty
p
e
s
/
n
rnb
.
h from typede
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoel
Removed types/nblist
.
h and ty
p
e
s
/
n
s
g
r
id
.
h from
t
yp
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
avid van
der Sp
o
e
l
Removed t
y
pes/mdatom
.
h
from typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
Removed ty
p
es/inputrec
.
h
f
rom type
d
efs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van
d
er Spoel
Fi
x
es bug in
t
he com
p
utation of Coef
f
icie
n
t of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der Spoel
Removed types
/
forcer
e
c
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
Davi
d
van der Spoe
l
Removed
i
nclude o
f
types/ifu
n
c
.
h
f
rom typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
avid van der Spoel
Rem
o
ved fou
r
i
n
cl
u
d
e
s
fr
o
m
legacyheaders/ty
p
ede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van
d
er Sp
o
el
Removed legacyheaders
/
types/com
m
rec
_
fwd
.
h from typede
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
D
avid van der
S
p
o
e
l
Moved conten
t
from m
d
run
.
h to s
e
parate
headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van d
e
r
Spoel
Remov
e
d <sys/types
.
h> and
"types/
c
onstr
.
h"
f
rom
t
ype
d
efs
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoel
Removed f
i
leio/trx
.
h from typ
e
de
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van
der Spoel
Moved
functions op
e
rating on forcerec to
separate head
e
r
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoel
Added
e
n
ergy (edr) file type to Options headers
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
vid van d
e
r Spoe
l
A
d
ded additional
constructor to Str
i
ngS
t
ream
c
lass
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David
van der Spoe
l
Mad
e
o
utput from
dumping
neightborl
i
sts easier to read
.
commit
|
commitdiff
|
tree
2015-07-31
David v
a
n der Spoel
Change initial param
e
te
r
s for testi
n
g expfit
.
commit
|
commitdiff
|
tree
2015-07-29
D
avid van der Spoe
l
Code
for checking xvg files i
n
tes
t
u
tils
.
commit
|
commitdiff
|
tree
2015-04-17
David van de
r
Spoel
Updated
exponential fitting
to make it rob
u
st
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoel
Clarifi
e
d comments f
o
r time-
d
ependent electric fields
.
commit
|
commitdiff
|
tree
2015-04-08
Davi
d
van de
r
Spoel
Fixe
d
incorrect output of gb_algorith as sa_algor
i
thm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der Spoel
U
p
date
d
doc
u
mentation for electric fields
.
commit
|
commitdiff
|
tree
2014-12-13
D
a
vid van d
e
r
Sp
o
el
Fo
u
r
n
ew quotes from around the world
.
commit
|
commitdiff
|
tree
2014-11-28
David van der Spoel
Fixes recent
l
y introduced bug in gmx anal
y
ze
.
commit
|
commitdiff
|
tree
2014-11-24
Dav
i
d van der Spo
e
l
Add
e
d w
a
rning
s
for ewa
l
d-geometry a
n
d
surface-epsi
l
o
n
commit
|
commitdiff
|
tree
2014-10-28
David van der Spoel
E
v
e
n
mo
r
e ref
r
e
shing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
David
v
a
n der Sp
o
el
Reo
r
g
ani
z
in
g
analysis of correl
a
t
ion fu
n
cti
o
ns
.
commit
|
commitdiff
|
tree
2014-09-23
Dav
i
d van der
S
poel
Fix
e
s pote
n
tial bug i
n
n
e
ighbors
e
arching
.
commit
|
commitdiff
|
tree
2014-09-17
David van de
r
S
p
o
e
l
Merge relea
s
e-5-0 into m
a
s
ter
commit
|
commitdiff
|
tree
2014-09-10
David van
der Spoel
Remove
.
tpa
,
.
tpb,
.
tp
x
,
.
trj
f
iles
.
Part of #1500
.
commit
|
commitdiff
|
tree
2014-08-30
David van der Spoel
Fixes issue with vsi
t
en a
n
d
v
erlet b
u
f
f
e
r
s
.
commit
|
commitdiff
|
tree
2014-07-05
David van der Spoel
Fixed inconsistency in blocka handl
i
ng
.
commit
|
commitdiff
|
tree
2014-06-29
Davi
d
van
d
er Spoel
Fixes #153
2
, SEGV in g_current
.
commit
|
commitdiff
|
tree
2014-06-25
D
a
vid van der
Spoe
l
A
d
ded
c
heck for domain
decomp
o
s
i
t
i
on an
d
shells
.
commit
|
commitdiff
|
tree
2014-06-24
Dav
i
d van der Spoe
l
A
d
ded c
h
eck in
gro
m
pp for shells an
d
i
np
u
t
r
e
c
i
s
sues
.
commit
|
commitdiff
|
tree
2014-06-22
David
v
an der Sp
o
el
Implemented fata
l
error fo
r
nst
c
al
c
energy!=1 with shells
.
commit
|
commitdiff
|
tree
2014-06-13
David
v
an der Spoel
Fix memory-usage error i
n
g_chi
commit
|
commitdiff
|
tree
2014-06-11
David van der
S
poel
F
i
xes bug wher
e
-e an
d
-dt f
l
ag
s
did not work
a
n
ymor
e
.
commit
|
commitdiff
|
tree
2014-06-07
David van der Spoel
Merge "Me
r
ge release-5-
0
into master"
commit
|
commitdiff
|
tree
2014-06-07
Dav
i
d
van d
e
r
Sp
o
e
l
Merge
r
elease-5-0 into master
commit
|
commitdiff
|
tree
2014-06-02
David van
d
er Spoel
Fi
x
ed wron
g
jour
n
al refe
r
ence in m
a
nual
commit
|
commitdiff
|
tree
2014-05-31
David
v
a
n
der Sp
o
el
Permit
trjc
o
nv to rea
d
and
w
rite vel
o
c
i
ties with
T
NG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David
v
a
n
de
r
Spoel
Fixes a comp
l
ic
a
ted
bug in g_anae
i
g
.
commit
|
commitdiff
|
tree
2014-05-15
Dav
i
d van
der Spoel
Added
cmake profili
n
g s
u
p
p
o
rt
commit
|
commitdiff
|
tree
2014-04-02
D
avid van der Spoel
R
e
mo
v
ed possib
i
lity of co
m
piling with
GSL
.
commit
|
commitdiff
|
tree
2014-03-31
David van der Spo
e
l
Fixed comp
i
l
ation issu
e
i
n
fgrid
.
cpp due to int/enum
commit
|
commitdiff
|
tree
2014-03-06
D
a
v
id van der Spo
e
l
Si
x
new qu
o
t
e
s from classic literature
.
commit
|
commitdiff
|
tree
2014-02-11
David v
a
n
d
e
r
S
poel
Fixed an
o
ther vmdio issue
.
commit
|
commitdiff
|
tree
2014-02-10
David van
d
er
S
poel
Moved
c
ondi
t
ional cma
k
e code for vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
David v
a
n
der S
p
o
el
Moved ra
n
dom number g
e
nerat
o
r
code to separate dir
.
commit
|
commitdiff
|
tree
2014-01-18
David van der Spoel
This patch moves the statistic
s
li
b
r
a
ry
t
o
it
s
own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
David van der
Spoel
This
p
a
tch moves preprocessing
h
ea
d
ers
t
o
g
m
xpreproces
s
commit
|
commitdiff
|
tree
2014-01-15
David
v
an der S
p
oel
This
patc
h
mov
e
s t
h
e nrama
.
[c
h
]
t
o th
e
gmxana dir
.
commit
|
commitdiff
|
tree
2014-01-13
David van
d
e
r
S
p
oel
C
leaned u
p
list of GROMAC
S
a
u
tho
r
s
commit
|
commitdiff
|
tree
2014-01-09
Dav
i
d
v
an
de
r
Spoel
Fixed p
r
eci
s
ion i
n
th
e
rmal expan
s
ion
c
o
e
ffic
i
ent calc
.
commit
|
commitdiff
|
tree
2013-12-23
David van der Sp
o
e
l
Fixed compilatio
n
issue due to gcc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
David van
der
Spoe
l
More Nobel
q
uotes an
d
others
commit
|
commitdiff
|
tree
2013-11-07
David van der Spoel
12 ne
w
quotes
commit
|
commitdiff
|
tree
2013-09-30
David va
n
d
e
r Spoel
Change name of gmxdump to dump and gmxch
e
c
k to c
h
eck
commit
|
commitdiff
|
tree
2013-09-29
David van d
e
r Spoe
l
Fixes bug
in
pro
c
essing virtual_sitesn
i
n
grompp
.
commit
|
commitdiff
|
tree
2013-09-26
D
avid
v
a
n
der Spo
e
l
Made MW of the
V
sit
e
partic
l
e
t
y
p
e
.
commit
|
commitdiff
|
tree
2013-09-21
Da
v
id van der Spoe
l
Moved
n
gmx to C++
,
renamed i
t
t
o view
.
commit
|
commitdiff
|
tree
2013-08-30
D
avid van der Spoel
Updated g
_
clust
e
r
commit
|
commitdiff
|
tree
2013-07-24
David van der Spoe
l
Fi
x
e
s
#
13
1
2 uninitialized error in g_ene
m
at
.
commit
|
commitdiff
|
tree
2013-07-17
Da
v
id
v
an der S
p
oe
l
A
d
ded citati
o
n to fre
e
vol
u
me
p
ap
e
r
.
commit
|
commitdiff
|
tree
2013-06-14
David van
der Spoel
Ne
w
analysi
s
tool
t
o comp
u
te the free volume and t
o
tal
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
David van de
r
Spoel
Fixe
s
#1194 error reading
4
.
5
.
5 tpr fi
l
e
s
wit
h
d
i
hres
commit
|
commitdiff
|
tree
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