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4.5.7 release
2013-04-19
M
i
chael Sh
i
rts
Some chan
g
es
for
m
d
-vv ex
t
racted from 4
.
6
commit
|
commitdiff
|
tree
2012-04-02
Michael Shirts
Fixes problems
with
g_msd and
g_energy
commit
|
commitdiff
|
tree
2011-09-05
Michael
S
hirt
s
Merge "
f
ixed i
n
corr
e
ct p
V
t
er
m
in t
h
e energy
f
ile"
.
.
.
commit
|
commitdiff
|
tree
2011-07-22
Michael Shirts
number o
f
degrees o
f
freedo
m
can be
f
r
a
c
tional
-- in
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael
Shirts
Additi
o
nal fixes to the nsttcouple a
n
d
n
stp
c
o
u
ple working
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael Shirts
Addi
t
i
o
nal
changes f
o
r
s
et
t
ing n
s
tt
c
o
uple
commit
|
commitdiff
|
tree
2010-08-19
Michael Shirts
Fi
x
for readir
.
c so that nstpc
o
uple and nsttcoup
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
M
i
chael S
h
irts
F
i
xed bug with
m
d-vv and with v-rescale
commit
|
commitdiff
|
tree
2010-08-19
Mi
c
hael Shirts
Prop
o
sed fix for v-rescale and berendsen f
o
r veloc
i
ty
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mi
c
hael Shirt
s
M
e
rge branc
h
'release-4
-
5-patches' of git@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shirts
Merge branch 'release-4-
5
-p
a
tches'
of
git@g
i
t
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shir
t
s
Me
r
ge
b
ranch 'release-4-5
-
patch
e
s' o
f
git@gi
t
.
grom
a
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael
S
hirts
Chang
e
d t
h
e
way energy con
s
ervati
o
n bookee
p
i
ng
is
done
.
commit
|
commitdiff
|
tree
2010-08-17
M
ichael Shirts
Merge branch 'release-4-5
-
patches'
o
f git@
g
it
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Michael
Shirts
Tryi
n
g to get vscale working
w
ith vv
.
commit
|
commitdiff
|
tree
2010-08-09
Micha
e
l Shirts
First pass at g
e
t
t
i
n
g VV
/
v-re
s
cal
e
formula cor
r
e
c
t
.
commit
|
commitdiff
|
tree
2010-08-07
Mich
a
el S
h
ir
t
s
Elimin
a
t
ed
s
om
e
commented o
u
t cod
e
.
commit
|
commitdiff
|
tree
2010-07-11
Michael Shirts
Fixe
d
initia
l
dis
p
lay of
temperature for md-vv-avek
commit
|
commitdiff
|
tree
2010-07-10
Michael Shirts
R
e
moved c++ style comm
e
nt
.
commit
|
commitdiff
|
tree
2010-07-10
Mich
a
el Shirts
Fi
x
ed
minor formatti
n
g conf
l
i
c
t
.
commit
|
commitdiff
|
tree
2010-07-10
Michael Shirts
Fix
i
ng t
h
e include fi
l
e definition for tro
t
ter_update
.
commit
|
commitdiff
|
tree
2010-06-27
Michael Shirt
s
Merge branch
'
m
as
t
er' of git@git
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-27
Michael Shi
r
t
s
Fixed gmx
_
membed
.
c to agree with domd
.
c
commit
|
commitdiff
|
tree
2010-06-27
Mi
c
hael Shirts
Restor
e
d
t
he f
o
rbidding
o
f nstca
l
cen
e
rgy for vv fo
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Michael Shirts
*
Started to
a
dd suppo
r
t
o
f
nstcal
c
e
n
ergy to vv versions
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
Mich
a
el Shir
t
s
Harded the shake cons
t
raint pa
c
kage so t
h
a
t
it
c
ouldn
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
M
i
c
ha
e
l Shi
r
t
s
Merge
branch 'mas
t
e
r
' of git@git
.
g
r
oma
c
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
El
i
minati
n
g
the
n
stcal
c
issue w
i
t
h
vv -- it should
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Mic
h
ael
S
h
i
rts
added
more
info
r
m
a
ti
o
n
in md
p
options
.
commit
|
commitdiff
|
tree
2010-06-12
Michael Shirts
Ra
i
sed the NH
C
HA
I
NLENGTH def
a
ult to
1
0
commit
|
commitdiff
|
tree
2010-06-11
M
i
c
hael
Sh
i
rts
Fix
e
d various lo
g
ic problems
p
reventing proper
e
nergy
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
M
i
c
h
ael Shirts
added a secondary chec
k
for error if the error is so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
M
ichael
S
hirts
M
e
rge bran
c
h 'mast
e
r'
of git@git
.
gromacs
.
or
g
:
g
romacs
commit
|
commitdiff
|
tree
2010-02-03
Mi
c
h
ae
l
S
hirts
Fix for memor
y
error
a
ffecting par
a
llel simulatio
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael
Sh
i
rts
A fi
x
to compute_bonds_lambda - th
e
value of nr_nonpert
u
r
b
ed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Mi
c
hael Shirts
R
evising the
i
t
e
ration of N
P
T for
single
p
recision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
M
ichael
S
hirts
Final
f
ix
f
o
r parall
e
l
c
h
e
ckpoint
i
ng with Nose-hoover
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Micha
e
l Shi
r
ts
Continuing f
i
xes for
c
heckp
o
int
i
ng in parallel
(also
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
M
i
chael Shirts
Merge branch 'master' of git@
g
it
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-22
Michael Sh
i
rts
A vari
e
t
y of
c
hanges
to correct
l
y do checkpointing
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michae
l
Shirts
Remo
v
e
d warning cau
s
ed by
thro
w
ing away 'const
'
definition
.
commit
|
commitdiff
|
tree
2010-01-18
Michael
S
h
irts
Fixes
for ent
r
y
t
o and r
e
ading extended sys
t
em variabl
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michael S
h
irts
A
d
d
ing back in changes that myst
e
r
iously
disappe
a
red
.
commit
|
commitdiff
|
tree
2010-01-17
M
i
chael Shirts
Revisio
n
s to harmonize velocity verl
e
t
w
i
th Berk's
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Micha
e
l Shirts
Fixe
d
typo in
changing name of nnhchains to nhchainleng
t
h
.
commit
|
commitdiff
|
tree
2010-01-11
Mi
c
hael Shirts
re
m
oved a dependency on a
file that did n
o
t e
x
ist
.
commit
|
commitdiff
|
tree
2010-01-11
Micha
e
l Shirts
changes
t
he nnhchains name to nhchai
n
length
commit
|
commitdiff
|
tree
2010-01-11
Michael Shi
r
ts
Merge
b
ra
n
ch
'ma
s
t
e
r' of gi
t
:/
/
git
.
g
r
omacs
.
or
g
/
g
romacs
commit
|
commitdiff
|
tree
2010-01-07
Michae
l
S
h
irts
Merge
bra
n
ch 'master' o
f
git://git
.
gro
m
a
c
s
.
o
r
g/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michae
l
Shirts
Merge br
a
nch 'm
a
ster' of git
:
//git
.
gr
o
macs
.
org/g
r
omacs
commit
|
commitdiff
|
tree
2010-01-04
Mic
h
ael Shirts
Commented out so
m
e
c
hecking
c
ode usef
u
l for t
h
e
future
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Mich
a
e
l
Shirts
Removed some legacy "#if 0"
c
od
e
.
commit
|
commitdiff
|
tree
2010-01-04
Mi
c
ha
e
l Shirts
Merge branch 'mast
e
r' of g
i
t@git
.
gromacs
.
org:
g
roma
c
s
commit
|
commitdiff
|
tree
2010-01-04
Michael Sh
i
rt
s
Improved out
p
ut in mdebin
.
c
commit
|
commitdiff
|
tree
2010-01-04
Michael Shir
t
s
No longer need to specify fe
p
-l
a
mbda every time --
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Michael
S
hirts
fix
e
s for handling p
e
rio
d
icity for dihedral restrain
t
s
.
commit
|
commitdiff
|
tree
2010-01-03
Michael
S
h
i
rts
re
m
oved c
o
de that had been
#ifdef'ed
o
ut
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shirts
Fixed the is
s
ues with the rest
r
ai
n
t
calculations
.
commit
|
commitdiff
|
tree
2010-01-02
Michael Shi
r
ts
Revisi
o
n of handling
o
f
foreign lambda bonds
.
commit
|
commitdiff
|
tree
2010-01-01
Michael Shirts
Fix for nonbondeds
.
commit
|
commitdiff
|
tree
2010-01-01
Micha
e
l Shirt
s
More fixe
s
for the multicomponent lambda
.
commit
|
commitdiff
|
tree
2010-01-01
Michael
S
hirts
Latest revision of fr
e
e energy changes
.
commit
|
commitdiff
|
tree
2009-12-29
Michael Shirts
Free
e
nerg
y
now apparent
l
y working with multilambda
.
commit
|
commitdiff
|
tree
2009-12-27
Michael Sh
i
rts
M
e
rge branc
h
'm
a
ster' o
f
git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-27
Michae
l
S
hirts
Merg
e
branch 'master' of git@gi
t
.
gromacs
.
or
g
:gromac
s
commit
|
commitdiff
|
tree
2009-12-24
Michael Shirts
Fix for in
i
tial energy
.
commit
|
commitdiff
|
tree
2009-12-23
M
ichael
Shirts
Merge br
a
nch 'master' of git@git
.
g
r
omacs
.
o
rg:g
r
omacs
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
F
ixed pres
s
ur
e
dispersion
correction order
.
commit
|
commitdiff
|
tree
2009-12-23
Mich
a
el Shirts
Merge branc
h
'ma
s
ter' of
g
it@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2009-12-23
Micha
e
l Shirts
fixed sd (I think)
.
commit
|
commitdiff
|
tree
2009-12-22
Michael Shirts
fixing
o
r
der of
DISPCORR
a
n
d
PRES
commit
|
commitdiff
|
tree
2009-12-22
Mic
h
ael Shirts
Merge branch 'master' of git
@
git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2009-12-22
Micha
e
l Shirts
Fo
r
ma
t
t
ing chan
g
e
s
for calc_dispc
o
r
r
commit
|
commitdiff
|
tree
2009-12-20
Micha
e
l Shirts
M
e
r
g
e bran
c
h 'master
'
of git@g
i
t
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-20
M
i
chael Shirts
Cl
e
anup a
f
ter last
c
ommit
.
commit
|
commitdiff
|
tree
2009-12-20
Michael Shi
r
ts
Fixed some pr
o
ble
m
s
w
ith
calcu
l
ation of d
i
spersion
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Mich
a
e
l Shirts
Merge b
r
a
n
ch 'master'
o
f git@
g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-20
M
ichael
S
h
i
r
ts
Made de
f
a
u
lt value of the nu
m
b
er of nose-
h
o
o
ver cha
i
n
s
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michae
l
Shirts
n
o
w
Nose-Hoov
e
r variables ar
e
w
r
i
t
ten to mdebi
n
only
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirts
Fixed an
i
ssue w
i
t
h
che
c
k
p
ointing not g
e
ttin
g
the
f
i
r
st
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michae
l
Shirts
Merge
b
ranch 'master' of git://git
.
gromac
s
.
org/gromacs
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
Commit
t
ing to m
e
rge
commit
|
commitdiff
|
tree
2009-12-19
Mich
a
el Shirts
commit
i
ng to merge
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
changed
output option
s
to b
e
more co
n
cise in
t
h
e
dispe
r
si
o
n
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
Some bu
g
fixes fo
r
t
h
e dis
p
ers
i
on co
r
rection
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shir
t
s
C
hanging the cpt f
i
le
number; c
a
n
'
t quite get
it t
o
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michae
l
Shirt
s
Changing the
cpt version; can't figu
r
e out h
o
w t
o
pr
e
serve
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Mi
c
h
ael Shirts
M
erg
e
b
ranch 'mast
e
r' of gi
t
@git
.
gr
o
m
ac
s
.
org
:
g
romacs
commit
|
commitdiff
|
tree
2009-12-19
M
ichael S
h
ir
t
s
Making th
e
code thread s
a
fe (removing the
stat
i
c ints
.
.
.
commit
|
commitdiff
|
tree
2009-12-17
Michael S
h
i
rts
Merg
e
bran
c
h
'm
a
ster' of
g
it@git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2009-12-17
Michael Shirt
s
adde
d
back in nosehoover_xi to tpr to avoid incompa
t
i
bilities
.
commit
|
commitdiff
|
tree
2009-12-17
M
i
c
hae
l
Shirts
Changed eiV
V
2 to
e
iVV
A
K
,
a
n
d
"
md-vv2" to "md-vv-avek
.
.
.
commit
|
commitdiff
|
tree
2009-12-05
Michael S
h
irts
fix
for rerun p
r
i
nting
commit
|
commitdiff
|
tree
2009-12-05
Michael Shirts
made some
o
utpu
t
fixe
s
.
commit
|
commitdiff
|
tree
2009-12-05
Mic
h
a
e
l
Shirts
Merge branch 'master' of
git@git
.
gro
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-04
Michael S
h
irts
trying to get para
l
lel versi
o
n
correct
.
commit
|
commitdiff
|
tree
2009-12-04
Mic
h
ael
S
hirt
s
Rewrite o
f
the half-step
e
kin f
o
r
v
elocity verlet,
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Mi
c
hael S
h
irts
More changes to g
e
t i
t
working wit
h
Ekin
A
veEkin
commit
|
commitdiff
|
tree
2009-11-30
M
i
chael
S
hir
t
s
Mor
e
fixes for cor
r
ect pres
s
ure wi
t
h EkinAveEkin
commit
|
commitdiff
|
tree
2009-11-30
Michael Shi
r
ts
C
ommitti
n
g another fix!
commit
|
commitdiff
|
tree
next