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Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4...
2010-08-06
B
erk Hess
M
erge branc
h
'rel
e
ase-
4
-5-patche
s
' of gi
t
@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
c
orrected the (irrelevant) default ir->gb_dielectric
_
offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
added -pbc option to g_tra
j
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
readinp, used for
e
.
g
.
mdp, no longer uses
g
mx
c
pp
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
ess
f
ixe
d
g
m
x_rmpbc undoing the
shifting
w
hen x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Be
r
k Hess
sc_sigm
a
n
o
w also se
t
s the m
i
nimu
m
value for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
make_ndx now allows ne
a
rly all cha
r
ac
t
ers in ato
m
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
g
m
x
c
heck now compar
e
s terms
b
y
n
ame match
i
ng
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k Hess
r
emoved commrec->n
t
hreads fr
o
m FAHCOR
E
code
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
gmxc
h
eck now
u
sing the diagonal f
o
r relativ
e
t
o
lerance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k Hess
fixed g_energy manual format
t
i
n
g issues
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
e
s
s
grompp automatic
n
stcalcen
e
rgy s
e
tting n
o
w takes
s
m
all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hes
s
adde
d
full precision option t
o
g_traj a
n
d
r
e
for
m
atted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk
Hess
fixe
d
PME communica
t
ion ran
g
e
when first DD
dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
erk Hess
m
ad
e
vres
c
a
l
e
an
d
B
ere
n
d
sen tc
o
up
l
e work
w
ith VV,
although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk He
s
s
corr
e
cte
d
LJ on H of charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
Berk Hes
s
c
omp
l
eted part
i
al rename of CY
N
t
o CYS f
o
r A
m
b
e
r
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hess
corrected the Amber aminoaci
d
s
.
r2b
f
iles
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
renamed
p
me_
m
axshift0/1
t
o
p
me_max
s
hi
f
t_x
/
y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
r
eplaced the Charmm
v
site parameters (wh
i
ch
w
ere OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
cor
r
ected a vsite parameter in t
h
e amber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected Cl
atom name
i
n amber ions
.
i
t
p
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber
ff atomtypes change: co
r
recte
d
mas
s
es, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
update of
am
b
er03 aminoacids
.
rt
p
, acciden
t
ally
l
eft
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k Hess
correc
t
ed mi
s
takes
i
n amber0
3
g
b
sa
.
it
p
commit
|
commitdiff
|
tree
2010-07-27
B
erk Hess
f
ixed typo in Mak
e
file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
m
o
ved ff_dum
.
i
t
p
to the gmx and
g
romos ff direct
o
ries
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
corr
e
c
t
ed the a
m
be
r
vsite paramet
e
rs
commit
|
commitdiff
|
tree
2010-07-27
Berk Hes
s
added
his to
opl
s
r2b file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made the
ff file
n
aming
of a
m
b
e
r and charmm consiste
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
c
o
r
re
c
te
d
the amber
water mod
e
l fil
e
s
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
ss
fixed PME decomposition check for inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
rena
m
ed
a
mber LYP
t
o L
Y
S and changed names for
w
ater
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
remove
d
HOH from amber rna
.
h
db
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added missing
e
ntries for
ambe
r
rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
cleaned up
Amber hdb
'
s
a
nd add
e
d HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
renamed
ato
m
types
fr
o
m amb
e
r99_? etc
.
to the ori
g
inal
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fixed PME com
m
unication ran
g
e (no
s
ilent errors)
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
remo
v
ed building block RT from the li
s
ts in shar
e
/
t
o
p
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
d
ded
residue and atom r
e
naming
f
or
AMBER dna and rna
commit
|
commitdiff
|
tree
2010-07-26
B
e
r
k Hess
a
d
ded DNA and RNA to the pdb2gmx
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
re
n
am
e
d O t
o
O2
i
n amber rna
.
r
t
p
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added natoms_force_const
r
to t_fo
r
c
e
rec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed O to O2 in
amber dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Be
r
k
H
e
s
s
removed garbage from checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (r
a
re)
i
ncorr
e
ct r
e
sidue
n
umbers w
h
en using gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
Hess
ad
d
ed
o
pe
n
m
m
w
r
app
e
r RF parameter checks
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
ess
minor
u
pdate to the pr
e
vios
appending fix
commit
|
commitdiff
|
tree
2010-07-19
Berk
Hess
fixed mdrun append check w
h
en req
u
ested
output file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Be
r
k
H
ess
adde
d
md
p
pa
r
am
e
ter for FE dH tables
commit
|
commitdiff
|
tree
2010-07-05
B
e
rk H
e
ss
changed the
d
efault
m
aximu
m
nu
m
b
e
r
of
b
ackups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
B
e
rk Hess
removed
a
lot of slow FFT grid sizes
f
rom calc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
e
r
k
Hess
docum
e
nte
d
pull cosine w
e
ig
h
ti
n
g
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
rename
d
md
r
un -cptnum to -cpn
u
m
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
ad
d
e
d m
d
run -cp
t
num option to keep
and number checkpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
reverted
a
cci
d
enti
a
l
c
h
an
g
e
o
f
ta
b
a
n
gles in
grompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
add
e
d includ
e
up
d
ate
.
h to couplin
g
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
a
dded
b
ack con
s
t
to gm
x
_sort
c
ompare
p
arams
f
o
r
qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Ber
k
Hess
r
emoved
obsolete fftgrid
c
ode and
disable
d
PPPM
with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
c
ha
n
g
e
d
pdb2gmx water model atom count det
e
ction
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
im
p
l
e
ment
e
d nsteps=-1
for md
r
un continuation
a
nd tpbconv
commit
|
commitdiff
|
tree
2010-06-24
Berk H
e
s
s
fixed
s
m
alloc
.
h and smalloc
.
c defini
t
io
n
in
c
onsi
s
tencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge branch
'mas
t
er'
of git@git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-23
Be
r
k Hess
remove
d
status
i
o
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk
Hess
f
i
x
ed
gmx
_
en
e
conv compi
l
er
wa
r
ning
s
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed eneconv -dt option temporaril
y
not writing averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
co
r
r
ected
edr f
o
rmat is
s
u
e
int
r
oduced
today
commit
|
commitdiff
|
tree
2010-06-21
Berk H
e
s
s
add gmx_qsort
r
ou
t
ine,
s
i
n
c
e
g
l
ibc qsort is not threa
d
safe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixe
d
typo in fatal_error call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now md
r
un do
e
s not write the trr
f
ile
wh
e
n it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk He
s
s
added env
var
GM
X
_MAXB
A
CKUP
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fix for
t
he previou
s
mdrun -rerun c
o
m
m
it
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
mdrun -rerun n
o
w re
a
ds the
r
erun traj only on the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
minor
update for pre
v
i
ous r
e
ple
x
bugfix
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hess
fixed
m
drun -rerun giving
N
aN with dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
adde
d
water model
selection
a
n
d
l
ist file to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-17
B
erk
H
e
s
s
made a sep
a
rate tips3p
.
it
p
file for CHAR
M
M
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k Hes
s
Merg
e
branch 'master'
o
f git
@
git
.
g
romacs
.
o
r
g:gr
o
m
a
cs
commit
|
commitdiff
|
tree
2010-06-16
B
erk
H
ess
added sp
c
e
to cha
r
mm27
commit
|
commitdiff
|
tree
2010-06-16
B
e
rk Hess
f
i
xed MPI crash
when nat_
h
ome=0
in DD
commit
|
commitdiff
|
tree
2010-06-16
B
erk Hess
res
t
ored the old order of the mdrun option and removed
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
replaced
m
ore gmx_fata
l
by coll
e
ctive cal
l
s in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
f
i
xed at
o
m naming in encad c-termi
n
i
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
with nst
e
ps=
-
1 m
d
r
u
n
n
ow prints
n
s/day
e
s
ti
m
ate
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
added nst
e
p
s
=
-1
o
ption to mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-16
Be
r
k Hess
al
l
energy
m
inimizers now do
0
s
t
eps w
i
th nste
p
s=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fixed incor
r
ect pd
b
2gmx CYS
2
to
CYS
r
enaming wh
i
ch
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk
H
es
s
all
v
sall loop
s
n
ow
t
rigge
r
pa
r
ticle decomposi
t
ion
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fata
l
_
e
rror in th
e
DD ini
t
ial
i
zation now c
a
lls MPI_F
i
n
a
lize
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
B
e
rk Hess
added -cwd opti
o
n to pdb2gm
x
commit
|
commitdiff
|
tree
2010-06-11
Berk
H
ess
fixed mdrun counter
resetting issues
commit
|
commitdiff
|
tree
2010-06-11
Berk Hess
op
t
imized the numb
e
r of t
h
rea
d
s
commit
|
commitdiff
|
tree
2010-06-10
B
e
rk Hess
made
D
D work properly wi
t
h all non
-
periodic system
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
added mo
r
e e
x
planation to i
d
ef
.
h
commit
|
commitdiff
|
tree
2010-06-10
B
erk Hess
fi
x
ed uni
n
iti
a
lized vari
a
ble i
n
d
o_md
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
f
ix
e
d
particle dec
o
mposi
t
ion
l
oad print
commit
|
commitdiff
|
tree
2010-06-04
B
e
rk Hess
fix
e
d pdb2gmx mes
s
ing
u
p coo
r
dinat
e
s w
h
en
d
e
let
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk
Hes
s
a
d
ded notes
o
n m
d
p
d
isre
p
aramete
r
s
commit
|
commitdiff
|
tree
2010-06-03
Berk
H
ess
distance restraint ense
m
ble averaging
i
s
no
longer
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Be
r
k Hess
f
ixe
d
bug in enum
par
s
ing error m
e
s
s
a
g
e
commit
|
commitdiff
|
tree
next