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fixed ga2la index for empty DD cells
2009-12-02
Berk H
e
ss
fi
x
ed
ga2l
a
index for e
m
pty DD cells
commit
|
commitdiff
|
tree
2009-11-19
Berk He
s
s
Merg
e
b
r
anch 'master' of
g
it@git
.
gromacs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2009-11-19
B
e
rk Hess
fixed
t
he g_rmsf
-
r
es option
commit
|
commitdiff
|
tree
2009-11-11
Berk Hess
fixed compiler warning
commit
|
commitdiff
|
tree
2009-11-11
Berk Hes
s
a
d
ded
e
xcl
u
sion s
u
p
p
or
t
for cg-cg l
o
ops
commit
|
commitdiff
|
tree
2009-11-11
Berk
H
ess
added exclus
i
on s
u
pport for
c
g-c
g
lo
o
p
s
commit
|
commitdiff
|
tree
2009-11-10
Ber
k
Hess
Merge branc
h
'
m
aster' of git@g
i
t
.
g
roma
c
s
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-11-10
Berk Hess
fixed g_ana
e
i
g
incorrect masse
s
f
o
r fitting
w
hen the
.
.
.
commit
|
commitdiff
|
tree
2009-11-06
Berk Hess
a
d
de
d
check f
o
r MPI support in init_mul
t
isystem
commit
|
commitdiff
|
tree
2009-10-20
B
e
rk Hess
fixed con
s
traint
error dump files not being written
.
.
.
commit
|
commitdiff
|
tree
2009-10-14
Berk Hess
made mdrun
-seppot work again
commit
|
commitdiff
|
tree
2009-10-08
Berk He
s
s
fixe
d
compiler warnings
commit
|
commitdiff
|
tree
2009-10-08
Berk
Hess
fixed
comp
i
ler w
a
rning
commit
|
commitdiff
|
tree
2009-10-08
B
erk H
e
s
s
sp
l
it force
.
c i
n
to forcerec
.
c and force
.
c a
n
d
added
.
.
.
commit
|
commitdiff
|
tree
2009-10-07
Berk Hess
fixed hang in MPI call
w
he
n
serial m
d
run was called
.
.
.
commit
|
commitdiff
|
tree
2009-10-07
Ber
k
H
ess
added
-ref and -fitxy op
t
i
o
ns
to g_rotmat
commit
|
commitdiff
|
tree
2009-10-07
Ber
k
H
es
s
added
e
nv
.
var
.
to remove charge groups
commit
|
commitdiff
|
tree
2009-10-07
Berk
H
ess
fixed
m
issin
g
energy
g
r
o
u
p ene
r
gies du
e
to inc
o
r
r
e
c
t
.
.
.
commit
|
commitdiff
|
tree
2009-10-02
Ber
k
Hess
made fil
e
appe
n
d
i
ng wor
k
a
gain
commit
|
commitdiff
|
tree
2009-10-02
Berk Hess
made pull
p
b
c
image cho
i
ce con
s
i
stent
f
or extreme disp
l
a
ceme
.
.
.
commit
|
commitdiff
|
tree
2009-10-02
Berk Hess
ad
d
e
d
ch
e
ck for user ta
b
le sp
a
cing
commit
|
commitdiff
|
tree
2009-10-01
Berk Hess
fixed pdb2gmx b
u
g when
a
ll
hydrogens in the N-terminus
.
.
.
commit
|
commitdiff
|
tree
2009-10-01
Berk Hess
r
e
moved s
p
a
c
e
in g
_
sgangle
y
-axi
s
unit
commit
|
commitdiff
|
tree
2009-10-01
Be
r
k Hess
co
r
r
ected g_sgan
g
le y-a
x
is unit
commit
|
commitdiff
|
tree
2009-09-30
B
e
r
k Hess
fixed
v
-site
pbc
b
ug
with
charge g
r
oups consis
t
i
ng
.
.
.
commit
|
commitdiff
|
tree
2009-09-30
Berk Hess
moved the
i
nitialization
o
f the grid ns l
i
sts
commit
|
commitdiff
|
tree
2009-09-30
Berk Hes
s
fixed bug w
i
th twin-
r
ange ns when not s
t
ar
t
ing a simulat
i
on
.
.
.
commit
|
commitdiff
|
tree
2009-09-28
Berk
H
e
ss
a
d
ded index group non-SOL,
rem
o
ved group
O
t
h
e
r
commit
|
commitdiff
|
tree
2009-09-25
Berk Hess
made
g
_
rotmat wo
r
k with le
s
s ato
m
s in
trx than in tps
commit
|
commitdiff
|
tree
2009-09-24
Berk Hess
fixed inco
r
rect #i
f
de
f
which did no
t
allow
vaccuum
.
.
.
commit
|
commitdiff
|
tree
2009-09-23
B
e
rk Hess
made g_sas rea
d
tps inst
e
ad of
t
px
commit
|
commitdiff
|
tree
2009-09-23
Ber
k
Hess
fixed ano
t
her issue wi
t
h
mdru
n
-rerun
w
ith a tp
r
without
.
.
.
commit
|
commitdiff
|
tree
2009-09-18
Berk Hess
fixed x
d
rd rese
r
ved word clash with fortran
commit
|
commitdiff
|
tree
2009-09-18
Be
r
k Hess
Mer
g
e branch 'master' of git
@
git
.
gromacs
.
o
rg
:
g
romacs
commit
|
commitdiff
|
tree
2009-09-18
B
e
rk Hess
added mo
r
e
opti
o
ns for f
r
e
e
-
e
nergy mo
l
ecu
l
e coupling
commit
|
commitdiff
|
tree
2009-09-18
Berk Hess
new f
e
atures for the t
e
rmini database:
r
eplace now
.
.
.
commit
|
commitdiff
|
tree
2009-09-17
B
erk Hess
a
dde
d
-r
m
sd
o
ption t
o
gmxcheck
commit
|
commitdiff
|
tree
2009-09-17
B
e
rk Hess
ma
d
e double preci
s
io
n
edr
file
detection mor
e
robu
s
t
commit
|
commitdiff
|
tree
2009-09-16
Berk
H
ess
fixed se
t
ting of bF
b
oolean
i
n trxframe
commit
|
commitdiff
|
tree
2009-09-15
Berk
Hess
ad
d
ed pull geom
e
tr
y
dista
n
ce_periodic and reorganized
.
.
.
commit
|
commitdiff
|
tree
2009-09-14
Berk Hess
added state_p
r
e
v
to mdrun
h
elp text
commit
|
commitdiff
|
tree
2009-09-14
Berk Hess
remo
v
ed unnece
s
sary
r
estrictions on pme
_
order
commit
|
commitdiff
|
tree
2009-09-10
B
er
k
Hess
c
h
a
nged pdb2gmx
-
nocmap option to
-
cmap
commit
|
commitdiff
|
tree
2009-09-09
Berk
H
ess
made the
nodecomm setup smarter
commit
|
commitdiff
|
tree
2009-09-04
Berk Hess
fixed incorrect min
d
ist output for
last residue with
.
.
.
commit
|
commitdiff
|
tree
2009-09-04
Ber
k
Hess
fixed g_nmens n
o
t writi
n
g trajectori
e
s
commit
|
commitdiff
|
tree
2009-09-04
B
erk Hess
fixed resnr increase
o
f
1 in confout
.
gr
o
commit
|
commitdiff
|
tree
2009-09-04
Berk Hess
proper out of ra
n
ge check
f
or sizeof(off_t)=4 and large
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Berk H
e
ss
made mdrun -multi wo
r
k again
commit
|
commitdiff
|
tree
2009-08-31
Berk Hess
f
i
xed memory ov
e
rallocation in genborn
.
c
commit
|
commitdiff
|
tree
2009-08-28
Berk Hess
added
t
ool
g_r
o
tmat
commit
|
commitdiff
|
tree
2009-08-28
Berk Hess
fix
e
d ind
e
x
group bug w
h
ich made it im
p
ossi
b
le t
o
sel
e
ct
.
.
.
commit
|
commitdiff
|
tree
2009-08-28
B
erk Hess
f
ixed crash in dom
d
ec with minimiza
t
i
on and removed
.
.
.
commit
|
commitdiff
|
tree
2009-08-26
B
e
rk H
e
ss
ad
d
ed
s
hi
f
ts to the GB
neig
h
b
o
r lists
commit
|
commitdiff
|
tree
2009-08-26
Berk He
s
s
fixe
d
the grompp che
c
k fro
m
GBSA parameters
commit
|
commitdiff
|
tree
2009-08-25
Berk Hess
added option -vel to tpb
c
onv
commit
|
commitdiff
|
tree
2009-08-25
Berk
Hess
fixed segv w
h
en readin
g
a ch
e
ckpoint file
into a trx
.
.
.
commit
|
commitdiff
|
tree
2009-08-25
B
e
rk Hess
r
emoved
erronous contribution
of
e
l
ec
t
ric fi
e
lds to
.
.
.
commit
|
commitdiff
|
tree
2009-08-24
Berk Hess
removed the co
m
m
-
mo
d
e check with SD and BD
commit
|
commitdiff
|
tree
2009-08-10
Berk Hess
chan
g
ed i/o of gmx_ste
p
_
t for possi
b
le issues with
.
.
.
commit
|
commitdiff
|
tree
2009-08-07
Be
r
k
H
ess
added env
.
var
.
to turn
o
ff t
h
e COM
p
ull viria
l
cont
r
ibution
commit
|
commitdiff
|
tree
2009-08-07
Berk
Hess
co
r
r
e
c
ted C
O
M pull position re
f
e
r
enc
e
to init+rate
.
.
.
commit
|
commitdiff
|
tree
2009-08-07
Berk Hes
s
adde
d
check for too
m
a
ny p
a
ramet
e
rs in
L
J
types sect
i
o
n
s
commit
|
commitdiff
|
tree
2009-08-06
Berk He
s
s
fixe
d
problems i
n
pd
b
2gmx with ch
a
in identifiers and
.
.
.
commit
|
commitdiff
|
tree
2009-08-06
B
e
r
k
Hess
add
e
d check
f
or Berends
e
n
tcoupl with REMD
commit
|
commitdiff
|
tree
2009-08-06
Berk Hess
removed dhdl_lr
f
rom
for
c
e
r
ec, no lon
g
er needed with
.
.
.
commit
|
commitdiff
|
tree
2009-08-05
B
e
rk Hess
updat
e
d addcon
f
for new tpx va
r
iables
commit
|
commitdiff
|
tree
2009-08-05
Berk
H
ess
f
i
xe
d
fa
t
al
error with
pbc and t
r
iclinic boxes
commit
|
commitdiff
|
tree
2009-08-05
B
e
r
k
Hess
added
c
hec
k
for
c
omm remov
a
l
commit
|
commitdiff
|
tree
2009-08-03
Berk Hess
changed t
h
e twin
-
range i
n
tegrator to
a symplect
i
c Trotter
.
.
.
commit
|
commitdiff
|
tree
2009-07-30
Be
r
k Hes
s
fixed in
c
orrect man
u
al layout
commit
|
commitdiff
|
tree
2009-07-29
Berk He
s
s
changed nan's to ze
r
o
s
f
or er
r
or estimates of constant
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Berk Hess
fixe
d
in
c
orre
c
t
d
Hd
l
output for bondeds, i
n
tr
o
du
c
ed
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Berk H
e
ss
fixed rlistlong fro
m
do_i
n
t
t
o do_real, in
t
ro
d
uced
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Berk Hess
updated th
e
energy file format to st
o
re a
v
erages over
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Berk Hes
s
remov
e
d some
l
o
a
d
c
ommunic
a
t
ion with -gcom
commit
|
commitdiff
|
tree
2009-07-14
Be
r
k
H
es
s
added mdp
par
a
m
e
ters
nstcalcenergy and
rlistlong
a
nd
.
.
.
commit
|
commitdiff
|
tree
2009-07-13
B
erk
Hess
fixed s
e
gv
in pd
b
2gmx
w
it
h
multiple (water)chai
n
s
commit
|
commitdiff
|
tree
2009-06-26
Berk Hess
m
o
ved the force wa
l
lcycle
_
stop from do
_
forcel
o
wlev
e
l
.
.
.
commit
|
commitdiff
|
tree
2009-06-26
Berk Hess
fixed incorrect connel
l
y su
r
fac
e
with
p
b
c
commit
|
commitdiff
|
tree
2009-06-26
Berk Hes
s
f
ixed seg
v
i
n
P
ME wit
h
mpirun -np 1
commit
|
commitdiff
|
tree
2009-06-26
B
e
rk Hess
fi
x
ed segv
i
n
PME with
mpiru
n
-
n
p 1
commit
|
commitdiff
|
tree
2009-06-26
Berk He
s
s
r
emoved MPI
calls
w
hen gmx_pa
r
a
l
l
el_env=0
commit
|
commitdiff
|
tree
2009-06-25
Berk Hess
fixed mi
s
sing communication of new
r
eppow
commit
|
commitdiff
|
tree
2009-06-24
Berk Hess
fixe
d
nrdf for T-couplin
g
being
incorrect
f
or more
.
.
.
commit
|
commitdiff
|
tree
2009-06-24
Be
r
k He
s
s
ch
a
nged g_traj summations from re
a
l to double
commit
|
commitdiff
|
tree
2009-06-24
Berk Hess
fixed the comm
.
bo
u
nd
c
y
cle
c
ou
n
t when not doin
g
D
L
B
.
.
.
commit
|
commitdiff
|
tree
2009-06-22
B
erk Hess
fixed th
e
division by
ze
r
o check
s
commit
|
commitdiff
|
tree
2009-06-22
Berk Hess
added
t
he repulsion p
o
w
er to the
t
pr
f
ile and added
.
.
.
commit
|
commitdiff
|
tree
2009-06-22
B
e
rk
Hes
s
fixed gm
x
_with
i
n
_tol being inco
r
r
e
ct f
o
r comparing
.
.
.
commit
|
commitdiff
|
tree
2009-06-22
Be
r
k Hess
re
m
oved memo
r
y allocation and print for
(n
o
n
e
xisting
.
.
.
commit
|
commitdiff
|
tree
2009-06-22
Berk
H
e
s
s
impl
e
mented resetting of all counte
r
s
a
nd removed th
e
.
.
.
commit
|
commitdiff
|
tree
2009-06-18
Berk
H
ess
added missing angle p
a
ramete
r
s
for ACE
commit
|
commitdiff
|
tree
2009-06-18
B
e
rk Hess
remo
v
e
d static var
i
ables
a
nd r
e
arranged some
d
a
ta str
u
c
tur
e
s
commit
|
commitdiff
|
tree
2009-06-18
Berk
Hes
s
made several
v
ariables const
commit
|
commitdiff
|
tree
2009-06-17
Berk Hess
remove
d
st
a
tic variables
commit
|
commitdiff
|
tree
2009-06-17
Berk Hes
s
i
mplemented fo
r
c
e
con
s
t
r
aining th
a
t work together
w
i
t
h
.
.
.
commit
|
commitdiff
|
tree
2009-06-17
Berk Hess
Merge branch 'maste
r
' of git@gi
t
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2009-06-17
B
erk
H
ess
fixed a seg
v
due to the recent cgi
n
fo c
h
a
n
g
e with mulitple
.
.
.
commit
|
commitdiff
|
tree
2009-06-16
B
erk Hess
fixed charged group mo
v
e too far er
r
or with triclinic
.
.
.
commit
|
commitdiff
|
tree
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