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Removed confusing gpp_atomtype functions.
2019-03-31
D
avid
v
an der Spoel
R
e
m
o
ved
c
o
nfusing g
p
p_atomtype functions
.
commit
|
commitdiff
|
tree
2019-02-18
David v
a
n
de
r
Spoel
Precision fix
for
rescbt code
.
commit
|
commitdiff
|
tree
2019-02-16
David
van
der Spoe
l
T
e
sts of restra
i
ned lis
t
ed p
o
tentia
l
s
.
commit
|
commitdiff
|
tree
2019-02-11
David van
d
er Spoel
Rem
o
ve buggy debug ou
t
put
.
commit
|
commitdiff
|
tree
2019-02-11
D
av
i
d
van d
e
r Spo
e
l
Tests for polarizati
o
n
f
unctions
.
commit
|
commitdiff
|
tree
2019-02-08
Da
v
id
v
a
n d
e
r Spoel
F
u
rthe
r
incre
a
se
o
f
tolerance f
o
r
angles
.
commit
|
commitdiff
|
tree
2019-02-08
D
av
i
d
van de
r
S
p
oel
Increased tole
r
ance
for angle f
u
nctions
.
commit
|
commitdiff
|
tree
2019-02-08
David van der Spo
e
l
Increase toleranc
e
in Angle test
.
commit
|
commitdiff
|
tree
2019-02-08
David van der S
p
oel
Tests for list
e
d forc
e
pote
n
tials
.
commit
|
commitdiff
|
tree
2019-01-26
David v
a
n
der Spoel
F
i
xed
s
ome ty
p
os
in com
m
ents
.
commit
|
commitdiff
|
tree
2019-01-17
David van
d
e
r
Sp
o
e
l
Allo
w
mu
l
tip
l
e c
o
ordinate sets
i
n listed_forces test
.
commit
|
commitdiff
|
tree
2019-01-17
David van
d
er Spoel
M
o
v
ed one regressiontest to co
r
e
gr
o
macs
.
commit
|
commitdiff
|
tree
2019-01-14
David va
n
der Spoe
l
MSD tests fo
r
t
h
e
-
mol option
.
commit
|
commitdiff
|
tree
2019-01-11
David van
d
e
r Spoel
Added
low
-
level
tests for impro
p
er dihedral
s
.
commit
|
commitdiff
|
tree
2018-12-31
David
v
an der Sp
o
el
Moved generic simulationdatabase code to test
u
tils
.
commit
|
commitdiff
|
tree
2018-12-30
David v
a
n
d
er
Spo
e
l
Moved inp
u
t
f
iles for te
s
ts to simulation dat
a
base
.
commit
|
commitdiff
|
tree
2018-12-30
David van
d
er Spoel
Im
p
lemente
d
native n
o
rm
a
l mode analy
s
is
t
ests
.
commit
|
commitdiff
|
tree
2018-12-22
Dav
i
d va
n
der Spoel
Revert "R
e
moved t_topology from g
m
x
m
s
d"
commit
|
commitdiff
|
tree
2018-12-20
David
van der Spoel
Remove
d
t_topology from gmx
m
sd
commit
|
commitdiff
|
tree
2018-12-05
David
van de
r
Sp
o
el
A
dded
n
ew testi
n
g cod
e
for normal mode ana
l
ysis
.
commit
|
commitdiff
|
tree
2018-12-04
David
van d
e
r
S
p
oel
S
m
al
l
update
t
o mdrun tests
.
commit
|
commitdiff
|
tree
2018-12-04
David van der Spoel
Remov
e
d gmx
m
orph
commit
|
commitdiff
|
tree
2018-12-04
David van der
Spoel
R
emoved gmx
d
y
ndom
commit
|
commitdiff
|
tree
2018-12-04
David van de
r
S
p
oe
l
Removed gmx anadock
commit
|
commitdiff
|
tree
2018-11-21
David van der Spoel
M
erge branc
h
'release-2019'
commit
|
commitdiff
|
tree
2018-11-18
David
van der Sp
o
el
Ad
d
ed citation for new
analys
i
s functionality
.
commit
|
commitdiff
|
tree
2018-11-11
David van
d
e
r Spoel
Fix entropy calculation in
gm
x
a
nae
i
g
commit
|
commitdiff
|
tree
2018-11-09
David
v
an d
e
r Spoel
C
hange get_atom_index to
allow
multi
p
l
e mo
l
e
cules
.
commit
|
commitdiff
|
tree
2018-10-11
David van d
e
r Spoel
R
ei
n
stated quasiha
r
monic e
n
tropy
calc
u
l
a
t
i
on in
gmx
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
David van der Spo
e
l
A
dded option
t
o
gmx nm
e
ig to pr
i
nt ZPE
.
commit
|
commitdiff
|
tree
2018-06-12
Da
v
id van der Spoel
Let gmx
n
meig print thermochem
i
stry
.
commit
|
commitdiff
|
tree
2018-03-21
D
a
v
id
van
d
er
Spoel
Renamed ent
r
opy
.
* to thermoc
h
em
i
stry
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van der
Spo
e
l
Split off ent
r
opy calculation
t
o separate file
.
commit
|
commitdiff
|
tree
2017-12-28
Davi
d
van der S
p
oel
Fixe
s
and u
p
da
t
es
for xplor2gml
.
pl an
d
atom_n
o
m
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David
v
an der
S
poel
Fixed
c
heck for wate
r
in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David van der S
p
oel
New mdp i
n
put
fo
r
electric fi
e
lds
.
commit
|
commitdiff
|
tree
2017-10-30
Dav
i
d
v
an
der S
p
oel
F
ixe
d
mdp
o
utput fr
o
m electric fiel
d
code
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spo
e
l
Adde
d
opti
o
n
-w
a
t
e
r tips3p
t
o pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David van der Spoel
Sp
l
it off the
N
MR relat
e
d an
a
lyses from
g
mx energy
.
commit
|
commitdiff
|
tree
2017-10-17
David van der Spoel
Fixed
m
issi
n
g ent
r
ies i
n
nrnb a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-15
David van der S
p
oel
Wor
k
e
d
around mis
s
ing Op
e
nMP
i
mplementation in
orires
.
commit
|
commitdiff
|
tree
2017-08-03
David van
d
e
r Spoel
Fix
e
d bug in gmx disres indexing
a
rr
a
ys
.
commit
|
commitdiff
|
tree
2017-08-02
David van
d
e
r
S
p
oel
Wo
r
ked around
missing OpenMP implementation in orires
.
commit
|
commitdiff
|
tree
2017-07-28
David va
n
der Spoel
A
dded unit
-
test f
o
r orienta
t
ion
r
estrai
n
ts output
.
commit
|
commitdiff
|
tree
2017-07-19
David
v
an der Spoel
Re
m
oved unnece
s
sary static declaration
s
fo
r
command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid van de
r
Spoel
Fixed test-order dependency in gm
x
preprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id van
d
er Spoel
Fix non-reproducability of
clu
s
tsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
Da
v
i
d
van de
r
S
p
oel
Xpm test for g
m
x clustsiz
e
commit
|
commitdiff
|
tree
2017-03-12
Da
v
id van der Spoel
Added tests for gmx
c
lustsize
.
commit
|
commitdiff
|
tree
2017-03-04
D
a
vid van der
S
poel
Removes ro
g
ue
prin
t
i
n
g to xvg file in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
David
v
a
n
der Spo
e
l
Fixes
b
u
g
in gmx solva
t
e with -s
h
el
l
that y
i
e
l
ded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David van de
r
Sp
o
e
l
Fixes SEGV
i
n
gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
David
van der S
p
oel
O
n
ly print all dangling atoms with grompp -v
commit
|
commitdiff
|
tree
2017-01-23
David va
n
der Spoel
Added reference for dihedral
f
u
n
cti
o
n in
O
PLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der Spoel
C
o
u
pl
e
of
n
ew quotes
commit
|
commitdiff
|
tree
2016-11-18
David van
d
er Spoel
Added first test
s
of bonded force
f
unctions
.
commit
|
commitdiff
|
tree
2016-10-14
D
avid van der S
p
oel
Fixes some mem
o
ry
l
eaks
a
sso
c
iated
w
it
h
testing applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avid van
d
er Spoel
Modularize
e
lectri
c
field handling
commit
|
commitdiff
|
tree
2016-09-27
David van
der
S
p
oel
Fixed
script xplor2gmx
.
pl to work with GMXDA
T
A
commit
|
commitdiff
|
tree
2016-09-26
David
van
d
e
r
Spo
e
l
F
i
xes issue with Re
l
ease build in c
o
rr
e
la
t
ion functions
.
commit
|
commitdiff
|
tree
2016-09-20
David va
n
der Spoel
Made
c
orrelation fun
c
tion routine use std::
v
e
c
tor
commit
|
commitdiff
|
tree
2016-08-24
David van
d
er S
p
oel
A
dde
d
documentation for shell pot
e
ntials
.
commit
|
commitdiff
|
tree
2016-08-03
Da
v
id van der Spoe
l
Thr
e
e
new quotes
.
commit
|
commitdiff
|
tree
2016-07-29
Dav
i
d v
a
n der Spoel
F
ixes
i
n
corr
e
ct
c
har
g
es in OP
L
S/AA-L fo
r
HISD a
n
d HISE
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van der Sp
o
el
In
t
roduce fatal error for too few frames in gmx
d
o
s
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Ma
d
e gmx d
o
s wo
r
k again
.
commit
|
commitdiff
|
tree
2016-06-22
Davi
d
va
n
der Spoel
R
e
moved sp
u
rious r_i
j
in f
o
rce for Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David van der Sp
o
el
Modi
f
y
lmfit library to avoid clashes wit
h
other
v
er
s
ion
s
.
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d van der
S
poel
Removed srenew that was making array smaller incorr
e
ctly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der Spoel
F
ixed divisio
n
by zero in
p
olarize
.
commit
|
commitdiff
|
tree
2016-01-20
David
v
an de
r
Spoel
Couple of
new quotes
commit
|
commitdiff
|
tree
2016-01-07
D
a
vid v
a
n der Spoel
Made norm
a
l modes work wi
t
h
s
hells and
v
s
ites
commit
|
commitdiff
|
tree
2015-11-24
Da
v
id
van der Spoel
F
i
x
e
s
ne
w
ly in
t
roduced bug in m
a
ke
_
ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David
v
an der Spoel
M
o
ved
d
omdec structures out
o
f commr
e
c
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Dav
i
d
van der Spoel
Cleanups in
le
g
acy
h
eader/
t
ypes/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
Dav
i
d
v
an der
S
po
e
l
M
e
rged legacyheaders/types
/
q
mmmrec
.
h i
n
t
o
mdlib/
q
mmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van
d
e
r Sp
o
el
Merged genborn
.
h from l
e
gacyhea
d
er
s
/
t
ypes into mdli
b
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Moved legacyhe
a
ders/types/group
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
M
e
rged l
e
gacyheaders/types/ns
.
h
an
d
nblist
.
h to mdtyp
e
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van de
r
Spo
e
l
Combine enums
.
h and nam
e
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spoel
Me
r
ge
d
lega
c
yheaders/nr
n
b
.
h and types/n
r
nb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David van der S
p
o
e
l
Mov
e
d mdato
m
.
h from
l
egacyheader/types
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van d
e
r S
p
oel
Mo
v
ed legacyheader
s
/types/energy
.
h to
m
dtypes
.
commit
|
commitdiff
|
tree
2015-11-15
D
a
vid van de
r
Spoel
Merged legacyhead
e
rs/ty
p
es/inputrec
.
h in
t
o mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David va
n
der Spoel
Merged legacyheaders/type
s
/state
.
h into m
d
types/sta
t
e
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der Spoel
R
e
pl
a
ced atom_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d va
n
der
Spoel
Mov
e
d
g
enbo
r
n
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
Da
v
id van d
e
r Spo
e
l
Move
d
txtdump
.
*
to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
Da
v
id
v
an der
S
poel
Moved copyrite
.
* to
f
ileio from g
m
xlib
a
n
d legacy
h
eaders
.
commit
|
commitdiff
|
tree
2015-11-11
David v
a
n
d
er Spoel
Moved in
p
utrec
.
* from g
m
xlib and legacy
h
e
a
d
e
rs to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-10
Da
v
id van der Spoel
Removed leg
a
c
y
headers/
t
ypedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
Da
v
id van der Spoel
M
oved df_hi
s
t
ory
utili
t
y routine
s
from ty
p
edef
s
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Davi
d
v
a
n der
S
poel
Repl
a
c
ed NOTSET fro
m
typedefs
.
h by
l
ocal solutions
.
commit
|
commitdiff
|
tree
2015-10-23
Davi
d
van der Spo
e
l
Removed en
e
rgyh
i
story
c
ode from
t
y
p
edefs t
o
a sepa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Sp
o
el
Moved pbc/cu
t
-off relat
e
d utilities from typedef
s
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Freed memory in legacy statistics routin
e
s
.
commit
|
commitdiff
|
tree
2015-10-03
Da
v
id v
a
n der Sp
o
el
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remov
e
d simp
l
e
.
h from nb_k
e
rnel_sse4
_
1_XX
commit
|
commitdiff
|
tree
2015-10-02
Davi
d
van der Spoel
R
emov
e
d
simple
.
h
from nb_k
e
rnel
_
sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
D
av
i
d van
der Spoe
l
Removed simple
.
h
f
rom
n
b_
k
e
r
ne
l
_
c
and n
b
_ker
n
el_sp
a
r
c64_hpc
.
.
.
commit
|
commitdiff
|
tree
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