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fixed segv in grompp due to gmxcpp not checking for #include statements without delim...
2010-11-24
Berk Hess
fixed
segv in gro
m
p
p due to gmxcpp not checking for
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Be
r
k Hess
added -
r
esnr option to ed
i
tconf
commit
|
commitdiff
|
tree
2010-11-09
B
erk Hess
f
ixed compile
r
warning in
pdb2gmx
.
c
commit
|
commitdiff
|
tree
2010-11-05
Berk Hess
pdb2gmx no
w
puts
a
tom
s
wit
h
cgnr=-1
in separate charge
.
.
.
commit
|
commitdiff
|
tree
2010-11-04
Berk Hess
Fixed md
.
log be
i
ng opened twice when appendin
g
, which
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Berk
H
e
ss
fixed
i
ncorrect print in fatal error on
charge group
.
.
.
commit
|
commitdiff
|
tree
2010-11-02
Berk Hess
proper defined of MAX_CHAR
G
EGROUP_SIZE=32 in a si
n
gle
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
Berk Hess
added HEM t
o
HEM
E
renami
n
g for Gro
m
os
and Cha
r
mm ff's
commit
|
commitdiff
|
tree
2010-10-28
B
e
rk Hess
fixed pdb2gmx chain mergin
g
bug (bugzilla 5
4
4
)
commit
|
commitdiff
|
tree
2010-10-26
Berk Hess
f
ixe
d
cycle print type cast issue on
c
e
rtain plat
f
orms
.
.
.
commit
|
commitdiff
|
tree
2010-10-21
Berk He
s
s
clarified make_ndx error message
commit
|
commitdiff
|
tree
2010-10-19
Berk Hess
changed
enx
i
o warning
i
nto fatal
e
r
rors by default
.
.
.
commit
|
commitdiff
|
tree
2010-10-18
Be
r
k
H
ess
fixed atom type n
a
me case for
m
ethan
o
l
.
itp in
g
r
omos43a1
.
ff
commit
|
commitdiff
|
tree
2010-10-18
Ber
k
H
e
s
s
f
ixed possible
o
ve
r
flow of unused va
r
i
a
ble in lincs
commit
|
commitdiff
|
tree
2010-10-18
Berk
H
ess
added che
c
ks for rare events that
would make vari
a
ble
s
.
.
.
commit
|
commitdiff
|
tree
2010-10-15
Berk Hess
mor
e
fixes f
o
r
T
PI wit
h
PME, now really fixed b
u
gzilla
5
90
commit
|
commitdiff
|
tree
2010-10-13
B
e
r
k
Hess
fixed g_v
e
lacc
-
m
no
t
automatically usin
g
-s
commit
|
commitdiff
|
tree
2010-10-12
Berk Hess
add
e
d n
o
te to g_densi
t
y for usi
n
g
g_energy fo
r
normal
.
.
.
commit
|
commitdiff
|
tree
2010-10-12
Berk Hess
fixe
d
i
n
correct dispe
r
sion correction for TPI with
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
B
e
r
k Hess
f
i
xed typo in checkpoint warn
i
n
g
commit
|
commitdiff
|
tree
2010-10-08
Ber
k
H
e
ss
made combinati
o
n of tpi and pme work a
g
ain in para
l
lel
commit
|
commitdiff
|
tree
2010-10-08
Berk Hess
f
ixed
c
ombination of
t
pic with pme, pm
e
mesh energy
.
.
.
commit
|
commitdiff
|
tree
2010-10-05
B
e
r
k
H
ess
made grompp mdp inpu
t
f
i
l
e
non-op
t
ional, f
i
xes bugzilla 577
commit
|
commitdiff
|
tree
2010-10-05
Berk Hess
added fail-safe c
h
e
ck for OpenMM with
doubl
e
precisio
n
commit
|
commitdiff
|
tree
2010-10-05
Berk Hess
renamed mdp s
e
ttin
g
A
c
e-approx to A
c
e-app
r
o
ximation
commit
|
commitdiff
|
tree
2010-10-05
Berk Hess
fixed com
p
lete
l
y incorrect pressure scalin
g
with nstlist
.
.
.
commit
|
commitdiff
|
tree
2010-09-30
B
erk H
e
ss
chang
e
d the grompp charge group radii to always
c
h
e
c
k
.
.
.
commit
|
commitdiff
|
tree
2010-09-25
Berk Hess
fix
e
d
ca
s
e
of op
l
s atom types i
n
shar
e
/top/ion
s
.
itp
.
.
.
commit
|
commitdiff
|
tree
2010-09-22
Berk Hess
add
e
d a
w
arning/note for
bond oscillatio
n
al periods
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Berk
H
es
s
added check
f
or t
a
u_t<=0
wi
t
h inte
g
r
a
tor
s
d
commit
|
commitdiff
|
tree
2010-09-21
B
e
rk Hess
fixed in
c
o
r
r
ect
g
m
xcheck c
o
m
parison of ir->separate
_
dhdl_file
commit
|
commitdiff
|
tree
2010-09-21
Berk H
e
ss
im
p
roved the initia
l
gue
s
s and
fitti
n
g weights
f
o
r
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Ber
k
Hess
removed
g
_
analyze co
n
fusing fitt
i
ng messages about
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Berk H
e
ss
fixed
t
oo small fixe
d
array in grompp
t
op reading
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Berk Hess
Re
v
ert "added GB non-polar s
o
l
v
a
t
ion ene
r
gy ter
m
t
o
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Ber
k
Hess
ad
d
ed GB non-polar
solvation energy term to the log
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
B
erk Hess
f
i
xed fre
e
-en
e
rgy g
i
v
ing
a fatal-error when GB12, GB
1
3
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Be
r
k Hess
added h
i
nt to g_traj
w
arning
commit
|
commitdiff
|
tree
2010-09-16
Berk
H
ess
fixed the maximum
print f
o
r
g
_
t
raj
-cv a
n
d -
c
f
commit
|
commitdiff
|
tree
2010-09-16
Berk He
s
s
fixed s
o
me min
o
r issues wit
h
g_
t
r
a
j -cv and -cf
commit
|
commitdiff
|
tree
2010-09-16
Be
r
k
Hess
tau_
t
=-1 no
w
works in gro
m
pp and with S
D
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
fixed g_traj segv when ran without
p
bc
commit
|
commitdiff
|
tree
2010-09-15
Berk
H
ess
fix
e
d charge gr
o
up radius LJ c
h
eck, whi
c
h could prod
u
ce
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
B
e
rk
Hess
added
m
issing F_PIDIHS c
a
se to t
o
p
s
ort free ene
r
gy
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
a
d
ded GMX_MAX_T
H
READS env
.
var
.
to se
t
the
m
aximum numb
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Ber
k
Hess
fixed
m
emor
y
all
o
c
ation and acc
e
ss issues
w
hen r
e
ad
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Ber
k
H
e
ss
grompp opti
o
n -pp now always writes to
cw
d
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
g_density n
o
w norm
a
lizes every fram
e
separate
l
y
commit
|
commitdiff
|
tree
2010-09-14
B
e
rk He
s
s
g_
d
ensity now normalizes with
t
he
a
verage volu
m
e in
s
te
a
d
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
fi
x
ed incorrect reference pos
i
t
ion
of po
s
i
tion res
t
r
aint
s
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
fix
e
d g
r
ompp -
t
f
rame choice for traj
e
ctories with
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
s
tat
e
switches b
e
tween
t
h
e cpt and tpr file in mdrun
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
B
erk H
e
ss
added chec
k
a
n
d warning for no velocities
in gro
m
pp
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
tur
n
ed on checkpoin
t
in
g
with nstlist=0
commit
|
commitdiff
|
tree
2010-09-10
Berk
Hess
re
m
oved
t
he l
o
wer b
o
un
d
check o
n
test
p
a
rticle insertion
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
removed tip5p from charmm27
.
ff/wate
r
model
s
.
dat, since
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
made
s
u
re t
h
e energy history
f
rom a checkpoint file
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Berk Hes
s
added SSE
o
verflow check for TPI
commit
|
commitdiff
|
tree
2010-09-09
Berk
H
ess
the
for
c
e
t
ables are now
continued l
i
n
e
arly from n
e
a
r
ly
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Ber
k
Hess
improved the automatic choic
e
of the number of
P
ME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk
Hess
added MCH3S a
t
om type
for Charmm
f
or
v
irtual
s
ites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
changed t
h
e order of the outer loops in
the fft
5
d transpose
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
B
erk
Hess
r
emove
d
e
mpty
e
dr
and x
t
c
f
iles wi
t
h n
m
commit
|
commitdiff
|
tree
2010-09-07
B
e
r
k
Hess
removed (nan)
a
verag
e
prin
t
i
ng with
n
ormal
mod
e
s
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
fixed crash with parallel nm with cu
t
-o
f
f's
commit
|
commitdiff
|
tree
2010-08-31
B
e
rk Hes
s
avoided creat
i
o
n
o
f
neighborlis
t
s wit
h
out j-
p
a
rticles
commit
|
commitdiff
|
tree
2010-08-26
Ber
k
Hess
fix
e
d
bug th
a
t c
a
used corrupted chec
k
point files
commit
|
commitdiff
|
tree
2010-08-26
Berk Hess
pdb2gmx now onl
y
a
l
lows
a mismatch of a s
i
gn (iso any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
f
i
xed
p
db2g
m
x usi
n
g s
t
art na
m
e iso end name for C-terminus
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fi
x
ed bug in se
a
rch_rtp introd
u
ced
i
n prev
i
o
us c
o
mmit
commit
|
commitdiff
|
tree
2010-08-24
B
e
r
k He
s
s
updat
e
d gmx_membed
.
c for
a V
V
upd
a
t
e
commit
|
commitdiff
|
tree
2010-08-24
B
e
rk Hess
fixed pdb2gmx
b
ehavior for nea
r
ly ma
t
ching residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k
Hess
removed the pdb2gm
x
-
c
wd option and updated the p
d
b2gm
x
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Ber
k
Hess
pdb2gmx
no
w
p
r
ints the fo
r
c
e fie
l
d di
r
befor
e
t
h
e selectio
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k
H
es
s
fixed mpi
h
an
g
/crash with sep
a
rate pme
n
ode
s
and dd
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
added function
d
o
_cpte_
n
_real
s
to check
p
oint
.
c
commit
|
commitdiff
|
tree
2010-08-20
Berk
Hess
f
ixed automa
t
ed DD/PME grid decomposition ch
o
i
c
e
w
hich
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
disabled optimiz
e
d
IBM BlueGene converts2ints macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k Hess
i
n
cr
e
ased tpx_gener
a
t
ion which
should
hav
e
bee
n
done
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k Hess
e
n
econv now copies t
h
e
new delta_t en
t
ry
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
a
d
ded dt to energy
f
ile
frames
commit
|
commitdiff
|
tree
2010-08-20
Berk H
e
ss
a
dd
e
d free and som
e
c
omment to deprecated
c
lose_trj
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
fi
x
ed segv's in g_an
a
e
i
g
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
reduce
d
the warning limit for
Berendsen T-coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
removed the b
N
EMD
b
oolean from
t
he
m
a
in MD lo
o
p and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added some comme
n
t
t
o
g
roup grom
p
p a
s
s
i
gnme
n
t options
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
add
e
d gr
o
up
comparis
o
n
to gmxcheck
and print
groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk
H
es
s
fixed pos
s
ible pathe
st
r
ing buffer o
v
erfl
o
w in
g
e
t
_lib
d
ir
commit
|
commitdiff
|
tree
2010-08-17
B
e
r
k
H
e
ss
adde
d
function
r
escale_velocities
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc now guesses
ePBC again for each
f
rame
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
gmx_r
m
pbc gets natoms
p
assed again, without natom
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
H
ess
put
o
mp p
r
agma's
i
n fft5d
.
c between ifdef'
s
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
added open
m
p pragm
a
's for the fft
5
d
t
ranspose routines
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed mdru
n
writes
t
pidist
.
xvg on all nodes
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
fixed segv in mdrun w
i
th
re
p
lica exchange
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k H
e
ss
fixe
d
fa
t
a
l
error
i
n mdrun fil
e
app
e
ndin
g
with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Be
r
k Hess
gmxcheck now p
r
ints rmsd
'
s as %g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hes
s
m
oved full precision real
format de
f
inition to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
B
e
r
k
Hess
rever
t
ed the last, non-co
s
metic
c
h
a
nge to
p
me
.
c
commit
|
commitdiff
|
tree
2010-08-12
Be
r
k Hess
minor cosmetic chang
e
s in pme
.
c
commit
|
commitdiff
|
tree
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