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fixed increasing memory usage with SHAKE and DD
2010-09-16
B
e
rk
Hes
s
fixed
t
he maximu
m
print for
g
_
t
r
a
j
-
cv a
n
d
-
cf
commit
|
commitdiff
|
tree
2010-09-16
Berk H
e
ss
fixed
some minor iss
u
es with g
_
traj -c
v
and -cf
commit
|
commitdiff
|
tree
2010-09-16
Berk Hess
tau_t=-1 now works in grompp and with SD
commit
|
commitdiff
|
tree
2010-09-15
Berk H
e
ss
fixed g_traj segv when
r
an w
i
thout pbc
commit
|
commitdiff
|
tree
2010-09-15
B
e
rk
H
ess
fix
e
d charge
g
roup radius
L
J
c
heck, which coul
d
prod
u
ce
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
added miss
i
ng F_PIDIHS case
t
o
t
opsort fr
e
e
energy
.
.
.
commit
|
commitdiff
|
tree
2010-09-15
Berk Hess
added GMX_MAX_
T
H
READS
e
nv
.
var
.
to set the maximu
m
number
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Be
r
k Hes
s
fixed memory alloca
t
ion
a
nd access issues when re
a
din
g
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
gromp
p
opt
i
o
n -pp now a
l
ways write
s
t
o
c
wd
commit
|
commitdiff
|
tree
2010-09-14
Berk
H
ess
g_density now normali
z
es every frame
s
ep
a
ratel
y
commit
|
commitdiff
|
tree
2010-09-14
Berk He
s
s
g_den
s
ity no
w
norma
l
ize
s
with the average v
o
l
ume
i
nstead
.
.
.
commit
|
commitdiff
|
tree
2010-09-14
Berk Hess
fixed incor
r
e
c
t reference posit
i
on of pos
i
tion re
s
traints
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk Hess
fixed gro
m
pp -t
frame choice for traject
o
r
i
es with
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Be
r
k
H
ess
state switch
e
s
between the cpt and tpr fi
l
e in mdr
u
n
.
.
.
commit
|
commitdiff
|
tree
2010-09-13
Berk
H
e
s
s
a
dded check
and
w
a
r
n
ing for no velocities in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
B
erk Hess
t
urned o
n
checkpointing w
i
th nstl
i
st=0
commit
|
commitdiff
|
tree
2010-09-10
Berk Hess
removed th
e
lower boun
d
check o
n
t
est par
t
icle insertion
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Be
r
k
Hess
r
emoved tip5p from ch
a
rmm27
.
ff/watermo
d
els
.
d
a
t, since
.
.
.
commit
|
commitdiff
|
tree
2010-09-10
Berk H
e
s
s
made sure th
e
energy histor
y
f
r
o
m a
checkpoint file
.
.
.
commit
|
commitdiff
|
tree
2010-09-09
Berk Hes
s
added SSE overflow check fo
r
TPI
commit
|
commitdiff
|
tree
2010-09-09
Berk H
e
s
s
the force tables
are no
w
continu
e
d line
a
rl
y
f
rom nea
r
ly
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk Hess
improved the au
t
o
matic ch
o
i
c
e
of the number of PME
.
.
.
commit
|
commitdiff
|
tree
2010-09-08
Berk He
s
s
added MC
H
3
S ato
m
type for
Charmm
f
or virtual sites
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
B
er
k
Hess
c
h
a
nged the order o
f
the ou
t
er loops
i
n
t
he fft5d tra
n
spos
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
re
m
ove
d
empty edr an
d
xtc fi
l
es with
n
m
commit
|
commitdiff
|
tree
2010-09-07
Ber
k
Hess
remov
e
d
(nan) a
v
e
rage pri
n
t
ing with nor
m
a
l
mod
e
s
commit
|
commitdiff
|
tree
2010-09-07
Berk Hess
f
i
xed crash
with parall
e
l nm with cut-off's
commit
|
commitdiff
|
tree
2010-08-31
Berk Hess
avoided creati
o
n o
f
neighborli
s
t
s wit
h
out j
-
p
a
rticles
commit
|
commitdiff
|
tree
2010-08-26
Be
r
k
H
ess
fixed bug
t
hat cause
d
c
orrupted checkpo
i
nt file
s
commit
|
commitdiff
|
tree
2010-08-26
B
e
r
k H
e
ss
pdb2
g
mx now only allows
a
mismatch of a sig
n
(
iso
any
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Berk H
e
ss
fi
x
ed
pdb
2
gm
x
using start name iso end
n
ame for C-term
i
nu
s
commit
|
commitdiff
|
tree
2010-08-24
Berk He
s
s
fi
x
ed
b
ug in search_rtp i
n
troduced in previous c
o
mmit
commit
|
commitdiff
|
tree
2010-08-24
B
erk
H
ess
updated gmx_membed
.
c for a VV update
commit
|
commitdiff
|
tree
2010-08-24
Berk Hess
fixed
p
db2
g
mx behavior for near
l
y m
a
t
ching residue
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Be
r
k He
s
s
r
emov
e
d
the pdb2gmx -cwd option a
n
d
upda
t
ed the pd
b
2gmx
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
pdb2g
m
x
n
ow prints
the force field d
i
r before
t
he
s
e
lectio
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Berk Hess
fixed mpi hang/crash with
separate pme
nodes and d
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hess
ad
d
ed function
d
o_cpte_
n
_
reals to
c
heckp
o
int
.
c
commit
|
commitdiff
|
tree
2010-08-20
Berk H
e
ss
fi
x
ed automat
e
d
D
D/
P
ME grid decomposition
choice w
h
ich
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk
H
e
ss
disabl
e
d
opt
i
mized IB
M
BlueGene converts2ints macro
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Be
r
k Hess
incre
a
sed tpx_generati
o
n
which
s
h
o
u
ld ha
v
e been d
o
ne
.
.
.
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
eneconv now copies the ne
w
d
e
lta_t entry
commit
|
commitdiff
|
tree
2010-08-20
Berk He
s
s
added
dt to energy file frames
commit
|
commitdiff
|
tree
2010-08-20
Berk Hes
s
a
d
d
ed
fre
e
an
d
some comment to depre
c
a
t
ed clo
s
e_trj
commit
|
commitdiff
|
tree
2010-08-20
B
e
r
k
Hess
f
i
xed segv's in
g
_
a
n
aei
g
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
reduced the warning limit
f
or B
e
r
e
n
ds
e
n
T-coupling
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
e
rk Hess
removed the
b
NEMD boolean from the main MD loop and
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hess
added
s
ome
comment to group
g
r
o
mpp as
s
ignment options
commit
|
commitdiff
|
tree
2010-08-18
Berk He
s
s
a
dded group co
m
p
a
rison
to g
m
xcheck and print groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
B
e
r
k Hess
f
i
xed po
s
sibl
e
pathe string buffer ov
e
rflow i
n
g
et_lib
d
ir
commit
|
commitdiff
|
tree
2010-08-17
Be
r
k
Hess
add
e
d function rescale_velocities
commit
|
commitdiff
|
tree
2010-08-16
Ber
k
Hess
gmx_rm
p
b
c
now guesses
ePBC
a
gain for each frame
commit
|
commitdiff
|
tree
2010-08-16
B
er
k
Hess
gmx
_
rmpb
c
gets natoms passed again, without na
t
oms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hes
s
pu
t
omp pragma's in fft5d
.
c
bet
w
een ifd
e
f's
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k
H
e
s
s
added openmp pragma's
for the fft5d
t
r
a
n
spose routines
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
fixed mdrun
w
r
it
e
s tpidist
.
xvg o
n
all nodes
commit
|
commitdiff
|
tree
2010-08-16
Berk He
s
s
fixed
seg
v
in
m
drun with repl
i
ca exchange
commit
|
commitdiff
|
tree
2010-08-16
B
erk Hess
fixed fatal error in mdrun file appending with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
gmxcheck now prints rmsd'
s
a
s
%
g
i
so %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
move
d
full precision re
a
l format
d
efinition to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk He
s
s
rev
e
rted the las
t
,
n
on-
c
o
smetic ch
a
n
g
e to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hes
s
m
i
n
or cosmetic c
h
anges in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
B
e
r
k Hess
ma
d
e the pdb2gmx
o
ccupancy
w
arning more
obvious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
fixed
incorrect pdb2gmx output with mu
l
tiple (altloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
rem
o
ved -m
e
rge from the pdb2g
m
x
manual
and
clarified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
fixed bug that c
a
u
se
d
a segv when sn
e
w failed
commit
|
commitdiff
|
tree
2010-08-10
B
erk He
s
s
removed CYS2 from
t
h
e
A
mb
e
r rtp
f
iles
commit
|
commitdiff
|
tree
2010-08-10
Berk
H
ess
removed pdb
2
gm
x
-
cysh hidden opt
i
on that sh
o
ul
d
h
a
v
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk
Hess
made mdrun -se
p
pot work w
i
th threads
an
d
-seppot n
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
Merge
branch
'release-4-5
-
patches'
of git@
g
it
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
erk Hess
corrected the (irrelevant)
d
efault ir
-
>gb_dielectric_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
added
-
p
bc option to g_traj
commit
|
commitdiff
|
tree
2010-08-05
B
erk Hess
readinp,
u
s
e
d fo
r
e
.
g
.
mdp,
n
o longer use
s
g
mxcpp
commit
|
commitdiff
|
tree
2010-08-05
B
erk
H
e
s
s
fixed gmx_rmpbc undoing the shifting when
x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Berk H
e
ss
sc_sigma now also set
s
the
m
i
nimum valu
e
for t
h
e so
f
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
make_ndx now allows
nearly
a
ll cha
r
ac
t
ers
in atom
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
gmxcheck now
c
o
mpar
e
s terms by nam
e
matc
h
ing
commit
|
commitdiff
|
tree
2010-08-04
Ber
k
Hess
r
e
moved commrec->nthre
a
ds from F
A
HCORE cod
e
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k He
s
s
gmxcheck
now using th
e
diago
n
al for
r
elati
v
e tol
e
rance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
fix
e
d g
_
energ
y
man
u
al
formatting issues
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
g
r
o
m
p
p
aut
o
matic n
s
tcalcen
e
rgy
s
e
t
ting n
o
w ta
k
es
sm
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
added full precision o
p
tion
t
o g_traj and ref
o
r
mat
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hes
s
fixed PME communication range when
first DD dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
made vrescale and Beren
d
se
n
t
c
ouple work with
V
V, altho
u
g
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
c
orrected LJ on H of charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Berk Hess
c
o
m
p
leted partia
l
rename o
f
CYN to
CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hes
s
c
o
rrecte
d
t
he Amber am
i
noacid
s
.
r
2
b files
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k
Hess
renamed pme_m
a
x
shi
f
t0/1 to
p
me_maxshift_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
repla
c
ed th
e
Charmm v
s
ite parameters (which were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
corre
c
t
e
d
a
v
site parameter in
t
he amber
ff's
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
H
ess
corrected C
l
atom name in amber io
n
s
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber ff a
t
omtypes c
h
ange
:
correcte
d
masses, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
updat
e
of amber
0
3
aminoacids
.
rtp, accidentally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected mistake
s
in amber03 gbsa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed ty
p
o in Makefile
commit
|
commitdiff
|
tree
2010-07-27
B
e
r
k
Hess
moved f
f
_dum
.
itp to the g
m
x and gromos ff dir
e
c
tories
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k Hess
corrected the am
b
er vsit
e
param
e
ters
commit
|
commitdiff
|
tree
2010-07-27
B
e
r
k H
e
ss
ad
d
ed his to opls r
2
b file
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk Hess
made
the ff file nami
n
g of amb
e
r and charmm
consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
cor
r
ect
e
d the amber water
model files
commit
|
commitdiff
|
tree
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