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MSD tests for the -mol option.
2019-01-14
Dav
i
d
v
a
n
d
e
r Spoel
MSD tests
for the
-mol optio
n
.
commit
|
commitdiff
|
tree
2019-01-11
D
avid v
a
n
d
e
r Spoel
Added
low-level tests fo
r
improper dihedral
s
.
commit
|
commitdiff
|
tree
2018-12-31
David van der Spoel
Moved generic simulationdatabase code to testutil
s
.
commit
|
commitdiff
|
tree
2018-12-30
David van der Spo
e
l
Move
d
input files for te
s
ts to simul
a
ti
o
n database
.
commit
|
commitdiff
|
tree
2018-12-30
David va
n
der Spoel
Implement
e
d nat
i
ve norma
l
mode anal
y
sis te
s
ts
.
commit
|
commitdiff
|
tree
2018-12-22
D
avid
v
an der
S
poel
Revert
"Removed
t
_topo
l
ogy
fro
m
gmx msd"
commit
|
commitdiff
|
tree
2018-12-20
Dav
i
d van d
e
r Spoel
Remo
v
e
d t_top
o
logy from gmx msd
commit
|
commitdiff
|
tree
2018-12-05
Davi
d
van d
e
r Spoel
Added new t
e
s
t
ing code for
n
o
r
m
al mode anal
y
si
s
.
commit
|
commitdiff
|
tree
2018-12-04
D
a
vid van der Spoel
Small
update to mdrun te
s
ts
.
commit
|
commitdiff
|
tree
2018-12-04
Da
v
id van der Sp
o
el
Removed
gmx mo
r
p
h
commit
|
commitdiff
|
tree
2018-12-04
David van d
e
r Spoel
Removed gmx dyndom
commit
|
commitdiff
|
tree
2018-12-04
D
a
vid van der Spoel
R
emoved gmx anadock
commit
|
commitdiff
|
tree
2018-11-21
David van der Sp
o
e
l
Merg
e
b
ranch 'relea
s
e
-2019'
commit
|
commitdiff
|
tree
2018-11-18
Da
v
id van
d
er
S
poel
Added citation for new analysis function
a
lity
.
commit
|
commitdiff
|
tree
2018-11-11
D
avid v
a
n der Spoel
Fix entropy calcu
l
ation in gmx a
n
aeig
commit
|
commitdiff
|
tree
2018-11-09
David van
d
er S
p
oe
l
Change
get_at
o
m_
i
ndex to allow multiple mo
l
ecules
.
commit
|
commitdiff
|
tree
2018-10-11
Da
v
id
van der Spoel
Re
i
nstated quasiharmonic
entropy ca
l
culatio
n
in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Da
v
id
v
an d
e
r S
p
o
e
l
Ad
d
ed option to gmx nmei
g
to print ZP
E
.
commit
|
commitdiff
|
tree
2018-06-12
David van de
r
Spoe
l
Let
gmx nmeig print t
h
ermochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
David van der
Spoel
Rena
m
ed ent
r
opy
.
* t
o
thermochemis
t
r
y
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der S
p
oel
S
p
lit off entropy calculati
o
n to separate file
.
commit
|
commitdiff
|
tree
2017-12-28
David v
a
n
der Spoel
Fixes and
u
pdate
s
for xplor2gml
.
p
l
an
d
a
tom_n
o
m
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David van
d
er
S
poel
Fixed ch
e
c
k
f
o
r water
i
n
g
en_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David van der Spo
e
l
Ne
w
mdp input f
o
r electri
c
fields
.
commit
|
commitdiff
|
tree
2017-10-30
Da
v
id van der Spoel
F
ixed
m
dp output from
electric fie
l
d code
.
commit
|
commitdiff
|
tree
2017-10-30
Dav
i
d
va
n
de
r
S
poel
Added option
-
wate
r
tips3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
Dav
i
d
v
a
n
der Spoel
Spl
i
t
o
f
f
t
he
N
MR related analyses from
gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
D
a
v
i
d
va
n
der Spo
e
l
Fixed
m
iss
i
ng e
n
tries in
nrnb
a
rrays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der S
p
o
el
Worked around missing
O
penMP implementat
i
on in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David van der Sp
o
e
l
Fixed bu
g
in
g
mx
disr
e
s indexin
g
arrays
.
commit
|
commitdiff
|
tree
2017-08-02
Dav
i
d v
a
n
d
e
r
Spoel
Worked around
m
is
s
ing OpenM
P
impleme
n
tation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
David van der Spoel
Added unit-test fo
r
orientat
i
o
n
res
t
raints
o
u
t
p
ut
.
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id van
de
r
S
poel
R
em
o
ved unn
e
cessary static declarations for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fixed test-orde
r
dependency in gmxprepro
c
ess tests
.
commit
|
commitdiff
|
tree
2017-07-19
David va
n
der Spoel
Fix
n
on-
r
eproducability o
f
clus
t
s
i
ze tests
.
commit
|
commitdiff
|
tree
2017-05-01
D
a
v
i
d
v
a
n der Sp
o
el
Xpm t
e
st for g
m
x clustsize
commit
|
commitdiff
|
tree
2017-03-12
Dav
i
d van
d
er Spoel
Added tests for
gmx clus
t
si
z
e
.
commit
|
commitdiff
|
tree
2017-03-04
Dav
i
d
van der Spoel
Removes
r
ogue p
r
inting to xvg fi
l
e
i
n
gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
David
v
an
d
er Spoel
Fixes bug in
gmx solvate
w
i
th -
s
hell that
y
ielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
Davi
d
van
der
Spoel
F
i
xes SEGV in gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
David v
a
n
der Sp
o
el
Only print all dangling atoms with grompp -v
commit
|
commitdiff
|
tree
2017-01-23
David van der Spoel
A
dded reference
f
or d
i
h
edra
l
fu
n
ction i
n
OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David
van der Spoel
Couple
of
n
ew quotes
commit
|
commitdiff
|
tree
2016-11-18
Dav
i
d
van der Spo
e
l
Ad
d
ed first tes
t
s
of bon
d
ed force
f
uncti
o
ns
.
commit
|
commitdiff
|
tree
2016-10-14
David van der Sp
o
el
Fix
e
s
some memory leaks associated with t
e
sting
a
pplied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van der
Spoel
M
o
d
u
l
a
r
ize electric field h
a
ndling
commit
|
commitdiff
|
tree
2016-09-27
David
v
an d
e
r Sp
o
el
Fixed script xplor2gmx
.
pl to work
w
ith GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
D
a
vid van der
S
poel
Fix
e
s
issue with Release
b
uild
i
n
correl
a
tio
n
func
t
i
o
ns
.
commit
|
commitdiff
|
tree
2016-09-20
David v
a
n der Spoel
Made correlation function routine
u
se std
:
:vec
t
or
commit
|
commitdiff
|
tree
2016-09-05
D
avid van de
r
Spoel
Merge "Merge branch release-2
0
16
"
commit
|
commitdiff
|
tree
2016-08-24
David van der Spoel
Added docu
m
enta
t
i
o
n for shell po
t
en
t
i
a
ls
.
commit
|
commitdiff
|
tree
2016-08-03
D
avid van der Spoel
T
h
ree new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
D
a
vid van der
Spoel
Merge "
M
er
g
e branch releas
e
-5-1 into releas
e
-20
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
D
avid van der Sp
o
el
Fi
x
es incorr
e
ct charges in OP
L
S
/
A
A
-
L
for HISD a
n
d
H
ISE
commit
|
commitdiff
|
tree
2016-07-08
D
avid v
a
n
der Spoel
Merge "Merge branch r
e
lease-5-1 into rele
a
se-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
Introduce fatal
error for too few frames
i
n
gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
D
avid va
n
der Spoel
M
a
d
e gmx
dos work a
g
ain
.
commit
|
commitdiff
|
tree
2016-06-22
David
v
an
der Spoel
Removed sp
u
rious
r
_ij i
n
force
f
or Morse potent
i
al
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van der Spo
e
l
Modify
l
mfi
t
li
b
rary to avoid clashes with o
t
her ver
s
ions
.
commit
|
commitdiff
|
tree
2016-03-23
David van der Spoel
Remov
e
d srenew that was ma
k
ing array
s
m
aller
inc
o
rrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David va
n
der Spoel
Fixed divis
i
on by zero in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David va
n
de
r
S
p
oel
Couple of ne
w
quotes
commit
|
commitdiff
|
tree
2016-01-07
David
van de
r
Spoel
M
a
de normal modes w
o
rk with shells and vsites
commit
|
commitdiff
|
tree
2015-11-24
David van de
r
S
p
o
e
l
Fixes newly in
t
roduced b
u
g in make_
n
dx
.
commit
|
commitdiff
|
tree
2015-11-23
Da
v
id va
n
der
S
poel
Mov
e
d domdec structures out of
c
ommre
c
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David v
a
n d
e
r Spoel
Cleanups in legacyhea
d
er/
t
y
p
es/comm
r
ec
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
avid van der Spoel
Merged
legacy
h
eaders/types/qmmmrec
.
h into md
l
ib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vi
d
v
an
d
er Spoel
Me
r
ged genbo
r
n
.
h from legacyheaders
/
types into mdl
i
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spoel
M
oved lega
c
yhe
a
ders/t
y
p
e
s/group
.
h
t
o
m
d
types
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Merged
l
egac
y
header
s
/t
y
pes/ns
.
h and n
b
list
.
h
to m
d
types
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spo
e
l
Combi
n
e enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid van der Spoe
l
Mer
g
ed leg
a
cyheade
r
s/nrnb
.
h and types/n
r
nb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spoel
Moved mdatom
.
h
from leg
a
cyheade
r
/ty
p
e
s to m
d
typ
e
s
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der
Spoel
Moved legacyheaders/t
y
pes/energy
.
h
to md
t
y
pes
.
commit
|
commitdiff
|
tree
2015-11-15
David van d
e
r
Spoel
Merged le
g
acyhead
e
rs/ty
p
es/in
p
utre
c
.
h
into
m
dtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van
der Spoel
Merged legacyheader
s
/types
/
s
t
ate
.
h into
m
dt
y
pes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
Re
p
laced
a
t
o
m_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
D
a
v
id van d
e
r
S
poel
Moved genborn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van der
Spoel
Moved txtdump
.
* to filei
o
.
commit
|
commitdiff
|
tree
2015-11-12
Davi
d
va
n
der Sp
o
e
l
Moved copyrite
.
* to fileio from gmxlib and le
g
acyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van der
S
poel
Move
d
in
p
utrec
.
* from gmxlib and legacyhead
e
r
s
to
md
t
y
p
es
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Rem
o
ved legacyhe
a
ders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David va
n
de
r
S
p
oel
M
o
v
ed
df
_
history utility ro
u
ti
n
e
s
from
t
ypede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der Spoel
Repla
c
ed NOTSET from typedefs
.
h by
local solut
i
ons
.
commit
|
commitdiff
|
tree
2015-10-23
D
avid v
a
n
d
e
r
Spoel
Remove
d
e
n
er
g
yhistory code from typedefs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
Da
v
id van der Spoel
Mo
v
e
d pb
c
/cut-
o
ff
relate
d
utilitie
s
from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
D
avi
d
van der Spo
e
l
Freed memory
i
n
lega
c
y stati
s
tics routines
.
commit
|
commitdiff
|
tree
2015-10-03
David
van der Spoel
Removed
s
i
mple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
moved si
m
ple
.
h from nb
_
kernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David v
a
n d
e
r Spoel
Removed si
m
ple
.
h from n
b
_
kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
vi
d
va
n
der Spoel
Removed simple
.
h
from nb_kernel_c
and nb_kernel_sparc6
4
_
h
pc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
Da
v
id van der Sp
o
el
Rem
o
ved include s
i
mple
.
h
f
rom
n
b_kernel_avx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Sp
o
e
l
Removed sim
p
le
.
h f
r
om nb_kernel_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
move
d
output_env_t,
n
ow using gmx_outp
u
t_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David va
n
de
r
Spo
e
l
Removed ty
p
e
s
/nrnb
.
h
f
rom
t
ypede
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d van der Spo
e
l
Rem
o
ved types/nblist
.
h an
d
types/nsgrid
.
h from
t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d
van der Spo
e
l
Remo
v
ed types/mdatom
.
h from typed
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
van der
S
p
oel
R
e
moved type
s
/
in
p
utr
e
c
.
h from ty
p
ed
e
fs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der
Spoel
Fixes bug in the computation
of C
o
ef
f
i
cient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
avid van der Spoel
Remove
d
types/force
r
ec
.
h from typedef
s
.
h
commit
|
commitdiff
|
tree
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