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Merge "Merge release-4-5-patches into release-4-6" into release-4-6
2011-09-05
Mi
c
hael Shir
t
s
Merge "fixed incorrec
t
pV term in th
e
energy file"
.
.
.
commit
|
commitdiff
|
tree
2011-07-22
Michae
l
Shirts
numb
e
r of de
g
rees of fr
e
e
d
om can be fr
a
ctional
--
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mich
a
el
S
h
i
r
ts
Additional fix
e
s to the n
s
ttcouple and n
s
t
pcouple working
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michae
l
Shirts
A
dditional changes for setti
n
g
nst
t
couple
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael
S
hirts
Fix for readir
.
c s
o
t
h
a
t nstpcouple an
d
nsttcouple
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael Shirts
Fixed bug w
i
th m
d
-v
v
an
d
with v-rescale
commit
|
commitdiff
|
tree
2010-08-19
M
ichael Shirts
Proposed fix for
v
-rescale and berend
s
e
n
for ve
l
ocity
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael Shirts
Merge bran
c
h 'release-4-5-
p
atch
e
s' of git@
g
i
t
.
g
r
om
a
cs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Mi
c
hael Sh
i
rts
Merge branch 'rel
e
ase-
4
-5-patches' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Micha
e
l
S
hirts
Merge br
a
nch
'relea
s
e
-4-5-patches' o
f
git@
g
it
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Mich
a
e
l S
h
irts
C
h
anged
the way
energy conservat
i
o
n
b
o
o
keeping
i
s do
n
e
.
commit
|
commitdiff
|
tree
2010-08-17
Michae
l
Shirts
Merge
branch
'r
e
l
e
ase-4-5-pat
c
hes
'
o
f
git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Michael Shir
t
s
Trying to
get vscale working with
vv
.
commit
|
commitdiff
|
tree
2010-08-09
Mi
c
ha
e
l Shirts
F
i
rst
pass at
g
etting VV
/ v-r
e
scale
formula correct
.
commit
|
commitdiff
|
tree
2010-08-07
M
i
chael
S
hirts
Eli
m
inated some
c
ommented
o
u
t
code
.
commit
|
commitdiff
|
tree
2010-07-11
Michael Shirts
Fixed initial display
o
f temperature for md-vv-ave
k
commit
|
commitdiff
|
tree
2010-07-10
M
i
chae
l
Shirts
R
emoved c+
+
sty
l
e
c
ommen
t
.
commit
|
commitdiff
|
tree
2010-07-10
Michael Shirts
Fixed minor
f
ormatting
conflict
.
commit
|
commitdiff
|
tree
2010-07-10
Mich
a
el
Shirts
Fixing t
h
e includ
e
file d
e
fin
i
ti
o
n for tro
t
ter_update
.
commit
|
commitdiff
|
tree
2010-06-27
Micha
e
l Shirts
Merge branch 'master
'
o
f
git@git
.
g
r
omacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-06-27
Mic
h
ael
Shirts
Fixed gmx_membed
.
c
to agree with domd
.
c
commit
|
commitdiff
|
tree
2010-06-27
Michael Shir
t
s
R
estored the forbidding o
f
ns
t
calcenergy for vv for
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Mic
h
ael
S
hirt
s
*Started to
a
dd suppo
r
t of nstcalcenergy to vv
v
ersions
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
Micha
e
l Shirts
Ha
r
ded the sh
a
ke constraint packag
e
so th
a
t
i
t co
u
ldn
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirt
s
Merge
branch '
m
aster' of git@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
Eliminati
n
g the nst
c
alc issue with
vv -
-
it should
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
M
i
chael Shir
t
s
added m
o
re information i
n
mdp opti
o
ns
.
commit
|
commitdiff
|
tree
2010-06-12
Michae
l
S
hirts
Raised t
h
e
N
HCHAINLENGT
H
default to 10
commit
|
commitdiff
|
tree
2010-06-11
M
ichael
S
hirts
F
i
xed
v
arious log
i
c problems preventing proper
ene
r
g
y
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
M
i
c
hael Shirts
added
a seco
n
d
a
r
y check for error if the error is so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Michael
S
hirt
s
M
e
rge
b
ra
n
c
h
'master
'
o
f git@git
.
g
romacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-02-03
Michael
Shirts
Fix for me
m
ory error affecting
p
arallel
simulations
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael Shirts
A fix t
o
co
m
pute_bo
n
d
s
_lambda - the v
a
lu
e
of
nr_nonperturbed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
M
i
c
h
ael Shirts
R
evisin
g
the itera
t
ion of NPT for single precision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
M
i
ch
a
el S
h
irts
Fina
l
fix
f
o
r
parallel check
p
o
inting with Nose-hoover
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Mich
a
el S
h
irts
Continuing fixes f
o
r check
p
o
inti
n
g in parallel (a
l
so
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirt
s
Merge br
a
n
c
h
'm
a
s
t
er'
o
f gi
t
@g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-22
Michael Shir
t
s
A variety of changes to
cor
r
ectly d
o
c
h
eckpointing
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Sh
i
rts
Re
m
oved warning
caused b
y
thro
w
ing away 'con
s
t' defini
t
io
n
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Shi
r
t
s
Fixes for ent
r
y to and reading
extend
e
d system
v
ariabl
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Mic
h
a
el Sh
i
rts
Adding bac
k
in changes that mysteriously disappeared
.
commit
|
commitdiff
|
tree
2010-01-17
Mi
c
hae
l
Shirts
Revisions to h
a
r
m
oniz
e
vel
o
city ver
l
et with Berk's
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Michael
S
hirts
F
i
xed typo in changing
n
ame of nnhch
a
ins to nhchainlengt
h
.
commit
|
commitdiff
|
tree
2010-01-11
Michael S
h
irts
removed
a
depend
e
ncy
on a file that d
i
d not exist
.
commit
|
commitdiff
|
tree
2010-01-11
Micha
e
l
S
hirts
c
h
a
ng
e
s the nn
h
chains
name to nhch
a
inlength
commit
|
commitdiff
|
tree
2010-01-11
M
i
chael Shirts
Merge bran
c
h
'master' of git://git
.
gro
m
ac
s
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Sh
i
rts
Merg
e
bra
n
ch 'master' of git://git
.
g
r
omacs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Shirts
Merge branch
'master'
o
f git://git
.
g
r
oma
c
s
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-04
Mi
c
hael
S
hirts
Commented o
u
t some
che
c
king code
us
e
ful for the f
u
t
ure
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Mi
c
h
ael S
h
irts
Remov
e
d
s
ome legacy "#
i
f 0" co
d
e
.
commit
|
commitdiff
|
tree
2010-01-04
Michael S
h
irt
s
Merge branch 'maste
r
' of git@git
.
gr
o
macs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-01-04
Michael
S
hirts
Impr
o
ve
d
o
utput
i
n mdebin
.
c
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
N
o
longer need to s
p
ecify fep-lambda
e
very time
-
-
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
ha
e
l S
h
irts
fixes for
h
a
ndling periodicity for dihedral restraint
s
.
commit
|
commitdiff
|
tree
2010-01-03
M
ichael Shirts
removed code that had bee
n
#ifd
e
f'ed out
.
commit
|
commitdiff
|
tree
2010-01-03
Michael S
h
irts
Fixed the issues with the restraint c
a
lculati
o
n
s
.
commit
|
commitdiff
|
tree
2010-01-02
Mic
h
a
e
l Shirts
R
e
v
ision
of h
a
nd
l
ing of foreign lambda bonds
.
commit
|
commitdiff
|
tree
2010-01-01
Michael Shirts
Fix f
o
r non
b
on
d
eds
.
commit
|
commitdiff
|
tree
2010-01-01
Mic
h
a
el Shirts
M
o
re
f
i
xes
f
o
r
t
he multicom
p
onent lambd
a
.
commit
|
commitdiff
|
tree
2010-01-01
M
i
chael
S
hirts
Latest revision of free
e
nergy
c
hanges
.
commit
|
commitdiff
|
tree
2009-12-29
Michael
S
hirts
Free ener
g
y now
a
p
p
arently
w
o
r
kin
g
with
m
ult
i
lambda
.
commit
|
commitdiff
|
tree
2009-12-27
Mi
c
hael S
h
irts
Merge br
a
nch 'master' of git@git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-27
Mic
h
ae
l
Shi
r
ts
Merge
b
ranch 'master' of gi
t
@git
.
gr
o
m
acs
.
o
rg:gro
m
acs
commit
|
commitdiff
|
tree
2009-12-24
M
i
ch
a
el Shirt
s
F
i
x for initia
l
ene
r
gy
.
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
M
erge branch 'm
a
ster' o
f
g
i
t
@git
.
g
r
oma
c
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2009-12-23
Mich
a
el Shirts
F
i
xed pressure dispersion c
o
r
r
e
ct
i
on order
.
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
M
erge b
r
a
nch 'master'
o
f
g
it@git
.
g
r
om
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-23
Mich
a
e
l
Shirts
f
i
xe
d
sd (I think)
.
commit
|
commitdiff
|
tree
2009-12-22
Michael Shirts
fixing o
r
der of DIS
P
CORR
a
n
d
PRES
commit
|
commitdiff
|
tree
2009-12-22
Mic
h
ael
S
h
i
r
ts
Merge branch 'master' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-22
Michael Sh
i
rts
Fo
r
matting changes for calc_dispcor
r
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirt
s
Merge branch 'master' of git@git
.
g
r
omacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirts
Cl
e
anup af
t
er
l
ast commit
.
commit
|
commitdiff
|
tree
2009-12-20
Michael S
h
irts
Fixed so
m
e problems with calculation of dispersi
o
n
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michael
Shirts
Merge branch 'maste
r
' of git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-20
M
ich
a
el Shirts
Made
def
a
ul
t
value of th
e
n
umbe
r
of nose
-
hoov
e
r chains
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Mich
a
el Shi
r
ts
now Nose-Hoover va
r
iables a
r
e written to mdebin o
n
ly
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
M
ichael Shirts
Fixed an issue w
i
t
h
ch
e
ckpointing no
t
getting the first
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Sh
i
rts
Merge branch 'ma
s
ter'
of git://
g
it
.
g
r
omacs
.
org/grom
a
c
s
commit
|
commitdiff
|
tree
2009-12-19
Mi
c
hael
S
hirts
Com
m
itti
n
g to mer
g
e
commit
|
commitdiff
|
tree
2009-12-19
Mich
a
el Shirts
co
m
miting
t
o merge
.
commit
|
commitdiff
|
tree
2009-12-19
Mic
h
ae
l
S
hirt
s
changed output
o
ptions to be more con
c
ise
i
n the dispersion
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Mic
h
ael Shirts
Some bu
g
f
i
xes for the dispersion
c
o
rre
c
tion
.
commit
|
commitdiff
|
tree
2009-12-19
M
ichael Shirts
Changi
n
g the cpt file nu
m
b
er; ca
n
't
q
uit
e
g
e
t it
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael S
h
irts
Chang
i
ng
t
h
e cpt version; can't
fi
g
ure out
h
ow to preserve
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
M
erge branc
h
'master' o
f
g
i
t@git
.
groma
c
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
M
a
king the code thread safe (removing
t
he st
a
t
ic int
s
.
.
.
commit
|
commitdiff
|
tree
2009-12-17
Michael Shirts
Merge
b
ranch 'mast
e
r' of
g
it@
g
it
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-17
M
ichae
l
Shirts
a
d
d
ed back in nosehoo
v
er_xi
to tpr to avoi
d
i
n
compatibilities
.
commit
|
commitdiff
|
tree
2009-12-17
Micha
e
l Shir
t
s
Chang
e
d eiVV2 to
e
iVVAK, and "md-vv2" to "md-vv-
a
vek
.
.
.
commit
|
commitdiff
|
tree
2009-12-05
Mich
a
e
l Shirt
s
fix
for rerun printing
commit
|
commitdiff
|
tree
2009-12-05
Michael Shirts
made some output fixes
.
commit
|
commitdiff
|
tree
2009-12-05
Mi
c
hael Shirt
s
Merge
branch 'maste
r
' of git@gi
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-04
Michael Sh
i
rts
trying to g
e
t paralle
l
version correct
.
commit
|
commitdiff
|
tree
2009-12-04
Micha
e
l
Shirts
Rewrit
e
of th
e
half-s
t
ep ekin for velocity v
e
rlet,
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michael
Shi
r
ts
M
o
re changes to get it working wi
t
h Eki
n
A
veEki
n
commit
|
commitdiff
|
tree
2009-11-30
Mic
h
a
e
l
Shirts
More fix
e
s
for correct p
r
ess
u
re
w
ith EkinA
v
eEkin
commit
|
commitdiff
|
tree
2009-11-30
M
ichael Shirts
Committing anot
h
er fix!
commit
|
commitdiff
|
tree
2009-11-30
Micha
e
l Shi
r
ts
Typo fix
.
commit
|
commitdiff
|
tree
2009-11-30
Michae
l
Shirts
Fixe
d
t
y
p
o -- correct |
t
o
||
commit
|
commitdiff
|
tree
next