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Let gmx nmeig print thermochemistry.
2018-06-12
D
avid
v
a
n
der Spo
e
l
Let
gmx nmeig
p
rint
thermochemistry
.
commit
|
commitdiff
|
tree
2018-03-21
Da
v
id van
d
e
r Spoel
Re
n
amed
e
ntr
o
p
y
.
* to
thermo
c
h
emistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
D
avi
d
van der Spoel
Split off entropy
c
alculation to separate file
.
commit
|
commitdiff
|
tree
2017-12-28
David van der Sp
o
el
Fixes
an
d
upd
a
tes for
xplor2gml
.
pl a
n
d ato
m
_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
D
avid v
a
n
d
er Spoe
l
Fixed check for water in gen_vsite
.
cp
p
commit
|
commitdiff
|
tree
2017-11-02
David van d
e
r
S
poel
New
mdp
inpu
t
for
electric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
Fixed mdp output from electric fiel
d
code
.
commit
|
commitdiff
|
tree
2017-10-30
David van der Spoel
Added option -
w
ater ti
p
s3p to pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-23
David va
n
der Spoe
l
Sp
l
it off the
NMR related analyses from gmx ener
g
y
.
commit
|
commitdiff
|
tree
2017-10-17
David van der Spo
e
l
Fixed missi
n
g entries in nrnb a
r
ray
s
.
commit
|
commitdiff
|
tree
2017-08-15
David van der Spoel
Worked around missing OpenMP imple
m
e
n
t
ation i
n
orir
e
s
.
commit
|
commitdiff
|
tree
2017-08-03
David van der Spoe
l
Fixe
d
bug
i
n
g
mx disres i
n
d
e
xing arrays
.
commit
|
commitdiff
|
tree
2017-08-02
David van
der Spoel
W
ork
e
d around missing OpenMP impl
e
mentat
i
on in orires
.
commit
|
commitdiff
|
tree
2017-07-28
David van der
Spoel
Added unit-test for ori
e
ntation re
s
t
r
ain
t
s out
p
ut
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Rem
o
ved unnece
s
sary static
d
eclar
a
tions for c
o
mman
d
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spo
e
l
Fixed test-or
d
er
d
ep
e
ndency in gmxprep
r
o
c
ess
t
es
t
s
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fix non-r
e
prod
u
c
a
bility
of
c
lustsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
Davi
d
va
n
der Spoel
Xpm test
f
or gmx clustsi
z
e
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoel
Ad
d
ed tests for g
m
x
c
l
ustsize
.
commit
|
commitdiff
|
tree
2017-03-04
David van
d
er
S
poel
Remo
v
es rogue printing to xvg file
i
n g
m
x mi
n
d
i
st
commit
|
commitdiff
|
tree
2017-02-27
D
avid v
a
n der Spoel
F
ixes bug in gmx solvate with -shell that yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
Davi
d
van der Spoel
F
i
xes SEGV in gmx
or
d
er
.
commit
|
commitdiff
|
tree
2017-02-02
D
avid va
n
der Spoel
Only print a
l
l
d
angl
i
n
g
atoms
w
i
th
grompp -v
commit
|
commitdiff
|
tree
2017-01-23
D
avid
v
an der Spoel
A
dded refere
n
ce
f
or di
h
edr
a
l function in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
Dav
i
d van der Spoel
Couple o
f
new qu
o
tes
commit
|
commitdiff
|
tree
2016-11-18
David van der
S
poel
Adde
d
fir
s
t
tests of bonded force
f
unctions
.
commit
|
commitdiff
|
tree
2016-10-14
David v
a
n
der Spoel
F
i
x
e
s some mem
o
ry
l
e
aks
associated with
t
esting applied
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
D
avi
d
van der
S
po
e
l
Modularize electr
i
c
f
i
eld handling
commit
|
commitdiff
|
tree
2016-09-27
D
a
v
id
van der Spoel
Fixed script xplor2gmx
.
pl to work with
GMXDATA
commit
|
commitdiff
|
tree
2016-09-26
David van der
S
po
e
l
Fixes issue with Release bu
i
ld in cor
r
e
l
ation fu
n
ctions
.
commit
|
commitdiff
|
tree
2016-09-20
David van der Spoel
Made corr
e
lation fun
c
tion r
o
uti
n
e use std:
:
vec
t
or
commit
|
commitdiff
|
tree
2016-09-05
David v
a
n der Spoel
Merge "Merge
b
ranc
h
release-2
0
1
6"
commit
|
commitdiff
|
tree
2016-08-24
David
va
n
d
e
r
Spoel
A
d
d
ed
docu
m
e
n
tation
fo
r
shell potentials
.
commit
|
commitdiff
|
tree
2016-08-03
Davi
d
van der Spoel
Three new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David van der Spo
e
l
M
e
rge "Merge branch release
-
5-1 in
t
o release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
D
avid van d
e
r S
p
oel
Fixes incorre
c
t cha
r
ge
s
in O
P
LS/AA-L for
H
ISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
David va
n
de
r
Spoel
Merge "Merge branch r
e
lease-5
-
1
into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van der S
p
oel
Int
r
oduc
e
f
atal e
r
ror for too
f
e
w
frame
s
i
n
g
m
x
dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van der
S
poel
Made gm
x
dos work
a
gain
.
commit
|
commitdiff
|
tree
2016-06-22
David va
n
der Spo
e
l
Removed s
p
urious
r_ij in force fo
r
Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Da
v
id van
der Sp
o
el
Mod
i
fy
l
m
fit lib
r
a
r
y to avoid clashes with
o
t
her vers
i
ons
.
commit
|
commitdiff
|
tree
2016-03-23
Da
v
id van der
S
p
oel
R
emov
e
d
s
renew that was making arra
y
smaller inco
r
rectly
.
commit
|
commitdiff
|
tree
2016-03-18
D
avid van der Spoel
Fixed division by ze
r
o in
polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David van
d
er Spoel
Couple
o
f new quotes
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoel
Made normal modes wor
k
with shel
l
s and vsi
t
es
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
Fixes n
e
wly in
t
roduced bug in make
_
ndx
.
commit
|
commitdiff
|
tree
2015-11-23
D
avid
v
an der Spoel
Moved domdec
s
t
r
uctu
r
es out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spoe
l
Cleanups in leg
a
cyheader
/
types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David va
n
der Spoel
Me
r
ged legacyheaders/types/qmmmrec
.
h
into mdl
i
b
/qmm
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vid van de
r
S
p
o
el
Merge
d
genb
o
r
n
.
h from
l
egac
y
h
eaders/types into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
Spoel
Moved leg
a
cyheaders/t
y
pe
s
/group
.
h
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Sp
o
el
M
e
rged leg
a
cy
h
eaders/types/
n
s
.
h and
nbli
s
t
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
e
r
Spo
e
l
Combine enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der Spoel
Merg
e
d legacyhe
a
ders/nrnb
.
h and types/nrnb
.
h to gmx
l
ib
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van
d
er Spoel
Moved mdatom
.
h f
r
o
m leg
a
c
y
he
a
der/type
s
to mdtyp
e
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
M
o
v
e
d le
g
ac
y
headers/types/
e
n
e
rgy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David
van der Spo
e
l
Mer
g
e
d
l
egacyh
e
ader
s
/types/i
n
put
r
ec
.
h i
n
to
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
van der Spoel
Mer
g
ed legacyheade
r
s/types/stat
e
.
h into mdtypes/stat
e
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van
d
er
Spo
e
l
Re
p
l
a
c
e
d atom_
i
d
by int
.
commit
|
commitdiff
|
tree
2015-11-13
D
a
v
id v
a
n
der Spoel
Moved genbor
n
.
h t
o
mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
a
vid van der Spo
e
l
Move
d
t
x
t
d
u
mp
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Moved copyrite
.
* to
fileio
f
rom gm
x
lib
a
n
d
legacyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David
v
an
d
e
r Spoel
Move
d
inputr
e
c
.
*
f
r
om gmxlib
and l
e
ga
c
yh
e
aders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
David van de
r
Sp
o
el
Remo
v
ed lega
c
yheader
s
/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der
Spoel
M
o
ve
d
df_his
t
ory
u
tility routines from
t
yp
e
defs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David v
a
n der Spoel
Replace
d
NOTSET fro
m
typedefs
.
h by
loc
a
l
s
o
lutions
.
commit
|
commitdiff
|
tree
2015-10-23
David van der Spoel
Removed energyhistory code from t
y
p
e
defs to a s
e
parate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
D
avid van der Spoel
Moved p
b
c
/cut
-
off r
e
l
a
ted utilities from type
d
efs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Freed memory
i
n legacy statisti
c
s routines
.
commit
|
commitdiff
|
tree
2015-10-03
Dav
i
d 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 n
b
_kernel_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van
d
e
r
Spoel
Re
m
oved simple
.
h from nb_kernel_sse2
_
XX
commit
|
commitdiff
|
tree
2015-10-02
Dav
i
d van der Spoel
Removed sim
p
le
.
h fr
o
m nb_kern
e
l_c
a
nd nb_k
e
rnel_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David
van der Spoel
Removed i
n
clude
s
imple
.
h
from nb_kernel_avx_1
2
8
_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avi
d
van d
e
r
Spoel
Remove
d
s
i
mple
.
h from nb_k
e
rnel_avx_
2
56_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van der
Sp
o
e
l
Removed
o
utput_env
_
t, now using g
m
x_ou
t
put_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
D
a
vid van
d
er S
p
o
el
R
e
moved types/nrnb
.
h
f
rom typedef
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoel
Removed types
/
nblist
.
h and type
s
/
n
sgrid
.
h
fro
m
t
y
pedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-30
Dav
i
d va
n
d
e
r Spoe
l
Remo
v
ed types/mdatom
.
h from typede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van
der S
p
oel
Remove
d
types/inputrec
.
h fro
m
typedefs
.
h and re
l
ete
d
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van d
e
r
S
poel
Fixes bug
i
n
the c
o
mputation of
C
o
e
ff
i
c
i
e
n
t o
f
Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David
va
n
der Spo
e
l
Removed types
/
forc
e
rec
.
h
f
r
om type
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der Spoel
Removed include
o
f t
y
pes/
i
fu
n
c
.
h from
typ
e
de
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Davi
d
van d
e
r Spoel
R
e
moved four includ
e
s
from l
e
ga
c
yheaders/ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid
v
an der Sp
o
el
R
emoved
l
egacyheaders/typ
e
s/commrec_fw
d
.
h from type
d
ef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
an d
e
r Spoel
Moved c
o
nte
n
t
f
rom mdrun
.
h to separate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David
v
a
n der Spoel
R
e
moved <sys/types
.
h>
and "typ
e
s/constr
.
h" f
r
o
m
t
ypede
f
s
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoe
l
Remov
e
d
f
i
leio/trx
.
h fr
o
m
typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
D
a
v
id van d
e
r Spoel
M
oved functions operating on forcerec to separate header
.
commit
|
commitdiff
|
tree
2015-08-28
D
av
i
d
v
an der Spoel
Add
e
d ene
r
gy
(
edr)
file
type to
Opt
i
ons
headers
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
vid v
a
n d
e
r
S
poel
Added additi
o
nal constructor to StringStream class
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van de
r
Spoel
Made
output fro
m
dumping neightborlists ea
s
ier to r
e
ad
.
commit
|
commitdiff
|
tree
2015-07-31
Dav
i
d van der
Spoel
Change ini
t
ial param
e
ters for testing
e
xpfi
t
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoel
Code for
ch
e
cking
x
vg files in
t
e
stutils
.
commit
|
commitdiff
|
tree
2015-04-17
Dav
i
d van der Spoel
Updat
e
d
exp
o
n
ential fitti
n
g to make it robu
s
t
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoel
Clarified com
m
ent
s
for time-
d
ependent elect
r
i
c
fields
.
commit
|
commitdiff
|
tree
2015-04-08
D
a
vid v
a
n
d
er Sp
o
e
l
Fixed
inco
r
rect
output of gb
_
al
g
orith as sa_
a
lgorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van
d
e
r
Spoel
Updated docume
n
t
ation f
o
r
electric fields
.
commit
|
commitdiff
|
tree
2014-12-13
David van der Spoel
Four
n
e
w
quotes
f
rom around the w
o
rld
.
commit
|
commitdiff
|
tree
2014-11-28
D
avid van der Spoe
l
F
ixes recently introduced bug in
g
mx analyze
.
commit
|
commitdiff
|
tree
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