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Refactored set_pbc_dd
2015-10-12
Micha
e
l Shir
t
s
Fix for lack of COM removal for md-vv
commit
|
commitdiff
|
tree
2015-08-18
Michael Sh
i
rt
s
F
i
x for expanded
e
nsemble
.
commit
|
commitdiff
|
tree
2015-04-30
Michael Shirts
Fix f
o
r ra
r
ely oc
c
uring
r
eplica
e
x
change error
.
commit
|
commitdiff
|
tree
2014-06-29
Mich
a
el Shirts
A
l
low pri
n
ting potentia
l
energies to dhdl
.
xvg
file
commit
|
commitdiff
|
tree
2014-04-21
M
i
c
hael Shirts
Issue
w
arni
n
gs for poten
t
i
a
l
s
witch w/
o
defining switch
.
.
.
commit
|
commitdiff
|
tree
2014-02-26
Mic
h
ael Sh
i
rts
Updatin
g
and
i
mproving Anders
e
n th
e
rmostat documentation
commit
|
commitdiff
|
tree
2014-02-06
Michael Shirts
EE dhdl header sho
u
l
d
not sp
e
ci
f
y
one lambda
commit
|
commitdiff
|
tree
2013-10-17
M
i
chael Shirts
Restarting from check
p
oint
n
o longer reinitialize
s
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirts
turning off expanded ensem
b
le for all
i
nte
g
r
ators bu
t
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Mich
a
el Shirts
Fixes a problem with pair type 2 int
e
rac
t
io
n
s with
.
.
.
commit
|
commitdiff
|
tree
2013-09-26
Michael Sh
i
rts
logic
f
i
x f
o
r
free energies with mdrun
-
rerun
commit
|
commitdiff
|
tree
2013-09-16
Mi
c
h
ael Sh
i
rts
Fixing
m
anual for
sc-coul descriptio
n
.
commit
|
commitdiff
|
tree
2013-08-02
Mi
c
hael Shirts
Fi
x
in
g
prob
l
em
c
aused
b
y
ove
r
flow i
n
exp
a
nded ense
m
ble
.
commit
|
commitdiff
|
tree
2013-06-20
Michael
S
hir
t
s
F
i
x
ing a problem whe
n
dhdl and re
p
lex
a
re not multiples
commit
|
commitdiff
|
tree
2013-05-30
Michael
S
h
irts
Fix
i
ng the
c
o
nstraint dhdl
t
erm i
n
shake
commit
|
commitdiff
|
tree
2013-05-26
Michael
S
hirts
Fi
x
of mem
o
ry
l
e
a
k
commit
|
commitdiff
|
tree
2013-05-21
Mic
h
a
el Shirts
Fix
e
d problem with b
o
nd cons
t
raint
dhdl b
e
ing
left out
commit
|
commitdiff
|
tree
2013-05-08
Mic
h
ael Shirts
fixing rerun wit
h
f
r
e
e
e
ne
r
g
y +
.
xt
c
or
.
g
ro
commit
|
commitdiff
|
tree
2013-04-30
Michael Shirts
Fi
x
ing handling of pertu
r
bation mass
c
hange
s
.
commit
|
commitdiff
|
tree
2013-04-26
M
ichael Shirts
Fixing a problem with
d
h/dl 1-4 interaction
s
commit
|
commitdiff
|
tree
2013-02-25
Michael Shirts
f
ix imc
o
mpatibility wit
h
t
p
r vers<64 wit
h
free energy
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
M
i
chae
l
S
h
irts
bugfix for md-vv + n
o
se-ho
o
v
er + (n
s
tcalcenergy > nsttco
u
ple)
commit
|
commitdiff
|
tree
2013-01-18
Michael
Shirts
Addendum for expanded e
n
sembl
e
optio
n
s plus
f
ormatting
.
.
.
commit
|
commitdiff
|
tree
2013-01-16
Michael Shirt
s
fixes issues with pressure cont
r
ol
a
nd infrequent ev
a
luation
commit
|
commitdiff
|
tree
2013-01-15
Michael Shirts
C
o
nti
n
uat
i
on
o
f
d
ocume
n
tation for
expande
d
en
s
emble
.
commit
|
commitdiff
|
tree
2013-01-13
Michael Sh
i
rts
Fi
x
es for
md-vv and rerun
commit
|
commitdiff
|
tree
2013-01-01
M
i
c
hael Shi
r
ts
F
i
x
ed a bug that
with
m
ultiple
exch
a
nges
commit
|
commitdiff
|
tree
2012-12-20
Michael Shirts
Fixes for
a
n
dersen temperature
c
ontro
l
commit
|
commitdiff
|
tree
2012-12-20
Michael
S
hirts
Fixes for expan
d
e
d
ens
e
mble a
n
d HREPEX
commit
|
commitdiff
|
tree
2012-12-20
Michael Shirts
Fix for the pressure in MTTK with
c
onstra
i
nts + di
s
persion
commit
|
commitdiff
|
tree
2012-12-14
M
i
c
ha
e
l Shirts
Fixes redmine issue #
1
071
commit
|
commitdiff
|
tree
2012-12-06
M
i
cha
e
l S
h
irts
Removing (inaccura
t
e
) virial temp
e
r
at
u
re calc
.
commit
|
commitdiff
|
tree
2012-11-27
Mi
c
hael Shir
t
s
R
e
m
o
v
es m
e
mory allocation fr
o
m fr
e
e energ
y
foreign
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Mich
a
e
l
Shirts
Cla
r
ification of m
d
p
_
op
t
, add
nst
e
xpand
defaults &
.
.
.
commit
|
commitdiff
|
tree
2012-10-12
Michael Sh
i
rts
Fixin
g
iss
u
es with replica e
x
c
h
ange
commit
|
commitdiff
|
tree
2012-07-31
Michael
Sh
i
rts
Added a check for efep that was missi
n
g
.
commit
|
commitdiff
|
tree
2012-07-29
M
ichael Shirts
Fix in when to call the co
n
s
t
raints for andersen
.
commit
|
commitdiff
|
tree
2012-06-29
Mi
c
hael Shirts
Mi
n
o
r formatting and con
s
iste
n
cy cha
n
ges to txt
d
ump
.
c
commit
|
commitdiff
|
tree
2012-06-29
Michael S
h
ir
t
s
Corrected checkpoint
v
ersion issues with free en
e
r
gy
.
.
.
commit
|
commitdiff
|
tree
2012-06-24
M
i
chael S
h
ir
t
s
Merge "Fix md
p
_opt formatting
o
f expand
e
d e
n
semble
.
.
.
commit
|
commitdiff
|
tree
2012-06-04
M
ichael
Shirts
Merging in
free energ
y
, exp
.
ensemble, & a
n
d
e
r
sen
t
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
M
i
ch
a
el
Shirt
s
Fixes pr
o
bl
e
ms with g_msd an
d
g
_
ener
g
y
commit
|
commitdiff
|
tree
2011-09-05
Mich
a
e
l Shirts
Merge "fixed incorrect
pV term
i
n
the
energy
f
ile"
.
.
.
commit
|
commitdiff
|
tree
2011-07-22
Michael Shirts
numbe
r
of de
g
r
ees
of fr
e
edom can be fractiona
l
-
-
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michae
l
Shi
r
ts
Additional f
i
x
e
s t
o
the
n
sttcouple and ns
t
pcouple wo
r
k
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael
S
h
irts
Additional chang
e
s for settin
g
nsttcoupl
e
commit
|
commitdiff
|
tree
2010-08-19
Michael Shirts
Fix for readir
.
c so that nstpcouple and
n
sttcoupl
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael Shirts
Fixed b
u
g with md-vv a
n
d with
v
-rescale
commit
|
commitdiff
|
tree
2010-08-19
Micha
e
l Shir
t
s
P
roposed fix fo
r
v-r
e
s
cale a
n
d
bere
n
dsen
f
or velo
c
ity
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael Shirts
Merge branch 'releas
e
-4-5-pat
c
h
es' of gi
t
@
g
it
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Micha
e
l Shirts
Merge branch
'
re
l
e
ase-4-
5
-patches' of
git@gi
t
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shirts
Mer
g
e b
r
anch 'release-4-5
-
p
atc
h
es' of git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shi
r
ts
C
h
a
n
g
ed the way energy
c
onservati
o
n bookeeping is
don
e
.
commit
|
commitdiff
|
tree
2010-08-17
Michael
S
hirts
Merg
e
branch 'relea
s
e-
4
-5-p
a
tches' of git
@
git
.
gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
M
i
chael Shirt
s
Trying to ge
t
vscal
e
w
orking w
i
t
h
vv
.
commit
|
commitdiff
|
tree
2010-08-09
M
i
c
hael Sh
i
rts
First pass at getting
V
V / v-r
e
scale f
o
rm
u
la cor
r
ect
.
commit
|
commitdiff
|
tree
2010-08-07
M
ichael Shir
t
s
Elimina
t
ed some comm
e
n
ted out code
.
commit
|
commitdiff
|
tree
2010-07-11
Micha
e
l
Shi
r
ts
Fixed i
n
i
tial display of
t
emperatu
r
e
for md-vv-avek
commit
|
commitdiff
|
tree
2010-07-10
M
i
chael
S
hirts
Remove
d
c++ style comment
.
commit
|
commitdiff
|
tree
2010-07-10
Mi
c
ha
e
l Shirts
Fixed mino
r
f
o
rmatting confl
i
ct
.
commit
|
commitdiff
|
tree
2010-07-10
M
i
c
hael Shi
r
t
s
Fixing the inc
l
ud
e
file defin
i
tion
for
trotter_u
p
da
t
e
.
commit
|
commitdiff
|
tree
2010-06-27
Michael Shirts
Merge branch
'mast
e
r' of git@git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-27
M
i
c
hae
l
Shi
r
t
s
Fixed gmx_membed
.
c
t
o
a
gree
w
ith do
m
d
.
c
commit
|
commitdiff
|
tree
2010-06-27
Michael Shir
t
s
Restor
e
d the forbidding of nstc
a
l
c
energy for
v
v for
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
M
ichael Shirts
*
S
tarte
d
t
o
add sup
p
ort of
n
s
t
c
alce
n
ergy to
v
v versio
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
M
ichael
S
h
irts
H
a
r
ded the sh
a
ke constraint package so that it co
u
ldn
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
M
i
c
hael Shirts
Me
r
ge branch 'master' of git@git
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-06-20
Michael S
h
irt
s
El
i
minating the nstcalc
i
ssue with vv -- it should
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Michael Shirts
add
e
d more info
r
mat
i
on in mdp o
p
tions
.
commit
|
commitdiff
|
tree
2010-06-12
Michael
S
hirts
Raised the
N
HCHAINLENGTH d
e
fa
u
lt
t
o 10
commit
|
commitdiff
|
tree
2010-06-11
Michae
l
Sh
i
rts
Fixed various logic pr
o
blems preventing pro
p
er
e
nerg
y
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
Michael Shirts
added a sec
o
ndary che
c
k fo
r
error
i
f
the e
r
ror is
so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Mic
h
ael Shirts
Merg
e
bran
c
h 'm
a
ster'
of git
@
g
i
t
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-02-03
Michael
Shirts
Fix f
o
r
m
em
o
ry
e
rror affecting parallel
sim
u
l
ations
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Mi
c
hael Shirt
s
A fix to compute_bonds_lambda - t
h
e
v
alue of
nr_nonper
t
urbed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
M
i
ch
a
el Shirts
Revis
i
n
g
the
iteration of NP
T
f
o
r single precision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
M
ichael Shirts
Final fi
x
for parallel checkpointing with Nose-hoover
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
M
i
c
h
ael Shirts
C
o
nti
n
uing fixes for checkpointing in
parallel (also
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
Merge branch 'master
'
o
f
git@
g
it
.
gromac
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirt
s
A variety o
f
c
h
a
nges
to c
o
r
r
ectly
do c
h
eckpointing
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Shirts
R
e
moved war
n
ing
c
ause
d
b
y thr
o
wing away '
c
onst'
d
efin
i
ti
o
n
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Shir
t
s
Fixe
s
f
o
r entr
y
to and re
a
d
ing
extended syst
e
m
v
ariables
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michae
l
S
hir
t
s
Adding back
in changes that mysteriously
d
i
s
appeared
.
commit
|
commitdiff
|
tree
2010-01-17
Michael
S
h
i
rts
Revision
s
t
o
harm
o
ni
z
e velocity v
e
rlet w
i
t
h
Berk's
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Mi
c
h
a
e
l Shirts
Fixed
t
ypo in changing name of nnhchain
s
to n
h
chainlength
.
commit
|
commitdiff
|
tree
2010-01-11
Michael Shirts
remo
v
ed a depe
n
de
n
cy on a file th
a
t did not exi
s
t
.
commit
|
commitdiff
|
tree
2010-01-11
Michael Sh
i
r
t
s
chan
g
es t
h
e
n
n
hchains name to nhch
a
in
l
ength
commit
|
commitdiff
|
tree
2010-01-11
Michael Shirts
Merge bra
n
c
h
'
master' of
git:
/
/git
.
gromacs
.
org/gr
o
macs
commit
|
commitdiff
|
tree
2010-01-07
Mic
h
ael Sh
i
rts
Merge
b
ranch
'm
a
ster' of git:
/
/g
i
t
.
gromacs
.
o
rg/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Micha
e
l Shir
t
s
M
e
rge branch 'm
a
ster' of
git://git
.
g
romacs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-04
Mi
c
hael Shirt
s
Comment
e
d
o
ut so
m
e chec
k
ing code useful for the f
u
ture
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Michae
l
Shi
r
ts
Removed some l
e
gacy "#if 0" code
.
commit
|
commitdiff
|
tree
2010-01-04
Michae
l
Shirts
M
e
rge bra
n
ch 'master' of git@git
.
groma
c
s
.
or
g
:
g
r
o
macs
commit
|
commitdiff
|
tree
2010-01-04
Mic
h
ael Shirts
Improved output
i
n
mdebin
.
c
commit
|
commitdiff
|
tree
2010-01-04
M
ichael Shi
r
t
s
No lon
g
er
need to specify fep
-
l
am
b
d
a every ti
m
e
-
-
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shirts
fixes
for h
a
ndling pe
r
iodicity for dihedral rest
r
aints
.
commit
|
commitdiff
|
tree
2010-01-03
Mich
a
el Shirts
removed code th
a
t had been #ifdef'
e
d out
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
hael
S
hirt
s
F
i
xed t
h
e issues with the
r
es
t
raint calculations
.
commit
|
commitdiff
|
tree
2010-01-02
Mi
c
hael Shi
r
ts
Revision of han
d
ling of foreign lamb
d
a b
o
nds
.
commit
|
commitdiff
|
tree
2010-01-01
Mich
a
el Shirts
Fix for nonbondeds
.
commit
|
commitdiff
|
tree
next