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corrected pdb2gmx rtp print conditional
2010-04-06
Berk
Hess
c
orrecte
d
pdb2gmx rtp print cond
i
ti
o
nal
commit
|
commitdiff
|
tree
2010-04-01
Be
r
k
Hess
added c
h
eck for NM and constraints
commit
|
commitdiff
|
tree
2010-03-30
Berk Hess
d
eprecated the En
c
ad forc
e
field
commit
|
commitdiff
|
tree
2010-03-30
Berk Hess
pdb2gmx now sorts the for
c
e field
a
lphab
e
tically
commit
|
commitdiff
|
tree
2010-03-30
Berk
Hess
pdb2gmx
n
ow also kee
p
s the re
s
i
d
u
e
n
a
me
s
C
Y
S, HEM and
HIS
commit
|
commitdiff
|
tree
2010-03-24
B
erk Hess
made g_dis
t
work
w
it
h
g
roups of a sing
l
e vsite
commit
|
commitdiff
|
tree
2010-03-23
Berk
H
ess
fix
e
d some valgrind
w
arnings
commit
|
commitdiff
|
tree
2010-03-12
Berk Hess
fixed non termi
n
ated
r
esname in pdb2gm
x
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
c
larified ch
e
ck
p
o
i
nt che
c
ksum mismatch mess
a
ges
commit
|
commitdiff
|
tree
2010-03-11
B
erk Hess
Mer
g
e
branch '
m
aster' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-11
Berk He
s
s
a
dded
m
issing include
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
shorten
e
d
t
oo long ener
g
y name
s
in md
.
lo
g
commit
|
commitdiff
|
tree
2010-03-10
B
erk Hess
fixed segv
w
ith NH and
p
d
commit
|
commitdiff
|
tree
2010-03-10
Berk Hess
fixed
hint in pdb
2
gmx war
n
ing
commit
|
commitdiff
|
tree
2010-03-09
Berk Hess
added checksums f
o
r mdrun xvg ou
t
p
u
t files
commit
|
commitdiff
|
tree
2010-03-09
Ber
k
Hess
fi
x
ed g_dip
o
lea av
e
raging
d
e
s
c
riptions
commit
|
commitdiff
|
tree
2010-03-09
B
erk H
e
s
s
minor fixes fo
r
last checkpoint upd
a
t
e
commit
|
commitdiff
|
tree
2010-03-08
Berk Hess
made m
d
run
f
ile
appending default and added
c
hecks
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
B
e
rk He
s
s
added g
m
x_fatal_
c
oll
e
ctive
and removed
gmx_f
a
tal
.
h
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
Berk Hess
genbox ca
n
now ins
e
rt multi-residue molecules
commit
|
commitdiff
|
tree
2010-03-05
Berk
H
ess
fixed bug
in c
o
n
s
train
t
s with
D
D
,
vacuum and nc=
2
commit
|
commitdiff
|
tree
2010-03-04
Ber
k
Hess
grou
p
e
d VV conditionals into one
c
o
n
ditional
commit
|
commitdiff
|
tree
2010-03-04
Berk Hess
fi
x
ed memory corruption with DD,
twin-range and constraints
.
.
.
commit
|
commitdiff
|
tree
2010-03-02
Berk Hess
added
option t
o
init_warni
n
g to turn all warning
s
in
t
o
.
.
.
commit
|
commitdiff
|
tree
2010-03-02
Berk
Hess
mo
v
ed all global
v
ari
a
bl
e
s for input file check
i
ng
.
.
.
commit
|
commitdiff
|
tree
2010-03-01
B
erk Hes
s
split off war
n
inp
.
c with
i
np
u
t reading wa
r
ning r
o
utines
.
.
.
commit
|
commitdiff
|
tree
2010-03-01
Berk
H
e
ss
ad
d
ed c
h
arge group size
check to grompp
commit
|
commitdiff
|
tree
2010-03-01
Berk H
e
s
s
split off
c
h
a
rgegroup
.
c
fro
m
pb
c
.
c
a
nd tpi
.
c from minimi
z
e
.
c
commit
|
commitdiff
|
tree
2010-03-01
B
erk Hess
c
o
rre
c
te
d
nrdf of froze
n
sett
l
e
d
mole
c
u
l
es
commit
|
commitdiff
|
tree
2010-02-25
Berk Hess
another precision correction for
g
_
bar
commit
|
commitdiff
|
tree
2010-02-25
B
erk Hess
corrected
the precision of
t
he g_bar
ou
t
put
commit
|
commitdiff
|
tree
2010-02-24
B
e
rk Hess
fixed pull constraint memor
y
error causin
g
a
lway
s
100
.
.
.
commit
|
commitdiff
|
tree
2010-02-24
Berk Hess
fixed i
n
correct w
a
llcycle count for
updat
e
commit
|
commitdiff
|
tree
2010-02-24
Berk Hess
fixed checkpoints
n
ot
b
ein
g
w
r
i
tten
commit
|
commitdiff
|
tree
2010-02-22
Berk Hess
g_bar
n
ow takes
c
orr
e
l
ation
s
along lambd
a
into acco
u
nt
.
.
.
commit
|
commitdiff
|
tree
2010-02-22
Berk He
s
s
added slope print for g_energy -sum
commit
|
commitdiff
|
tree
2010-02-22
Berk Hess
cor
r
ec
t
ed NH va
r
iables wh
e
n
reading old tpx and cpt
.
.
.
commit
|
commitdiff
|
tree
2010-02-17
Berk Hess
some clean-
u
p
in the
V
V
co
d
e
in do_m
d
an
d
fixed
t
h
e
.
.
.
commit
|
commitdiff
|
tree
2010-02-17
Berk
H
e
s
s
sy
n
c
hron
i
zed
c
heckpo
i
nting and ter
m
i
nation with md
r
u
n
.
.
.
commit
|
commitdiff
|
tree
2010-02-16
B
e
r
k
Hess
fixed
a typo in an
e
rror message
commit
|
commitdiff
|
tree
2010-02-16
Ber
k
H
e
ss
md
r
un now also checks -npme wit
h
non-
p
arallel compilation
commit
|
commitdiff
|
tree
2010-02-16
Berk Hess
a
dded check for mdrun
-d
d
and
-
npme
w
ithout parallel
.
.
.
commit
|
commitdiff
|
tree
2010-02-16
B
erk
Hess
f
i
xed glob
a
l
s
ignaling with VV
commit
|
commitdiff
|
tree
2010-02-15
B
er
k
Hess
colle
c
ted all
th
e
mdrun
parallel s
i
gnals in
t
o one d
a
ta
.
.
.
commit
|
commitdiff
|
tree
2010-02-15
Berk Hess
fixed d
e
adlocks
d
uring checkpoi
n
tin
g
a
nd termination
commit
|
commitdiff
|
tree
2010-02-15
Berk Hess
made mdrun npme guessing work more co
n
sistently
commit
|
commitdiff
|
tree
2010-02-15
Berk Hes
s
f
ixed output size
e
stima
t
es for energy
and dhdl
f
ile
s
commit
|
commitdiff
|
tree
2010-02-15
Ber
k
H
ess
ma
d
e re
a
d
_
x
vg i
g
nore
a
last non newline
t
erminated
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
Berk Hess
fixed
possible mdru
n
repetit
i
v
e
war
n
ing print with
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
Berk Hess
fixed tem
p
erature issu
e
in
t
roduced in t
h
e l
a
st commit
commit
|
commitdiff
|
tree
2010-02-11
Berk Hess
made gen
i
on operate on the
last solvent entry in
t
op
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
replaced the greek x
v
g symb
o
l
escape se
q
uences in g
m
xlib
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
made g_
b
ar rea
d
t
h
e temperature for
t
he
d
h
dl
.
xvg files
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
changed
-
x
v
g
r bool o
p
ti
o
n t
o
-xvg enum xm
g
race/xmgr
.
.
.
commit
|
commitdiff
|
tree
2010-02-09
Berk Hess
fixed inc
o
rrect virial
w
he
n
n
stcalcen
e
rgy>0 and epc=no
commit
|
commitdiff
|
tree
2010-02-08
Berk H
e
ss
c
h
a
n
ged g_e
n
ergy
-
a
ver t
o
print the average i
s
o the sum
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
fixed drif
t
in g_en
e
rgy, bro
k
e
a
few
commits
a
go
commit
|
commitdiff
|
tree
2010-02-08
Berk Hes
s
in
t
ro
d
uced STEP
S
TRSIZE fo
r
prin
t
ing gmx_larg
e
_int_t
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
changed g_energy
and g_bar error estimation to average
.
.
.
commit
|
commitdiff
|
tree
2010-02-05
B
erk
H
e
s
s
clean
e
d
u
p
the g_energy energy storage and added er
r
o
r
.
.
.
commit
|
commitdiff
|
tree
2010-02-04
Berk Hess
added unit for
g_en
e
rgy -sum
commit
|
commitdiff
|
tree
2010-02-04
Ber
k
Hess
add
e
d missing incl
u
de
commit
|
commitdiff
|
tree
2010-02-04
Be
r
k Hes
s
m
a
de i/o
e
rror
checking in
g
m
x
cpp stricter
commit
|
commitdiff
|
tree
2010-02-04
Berk Hes
s
fixed a
m
emory leak in
g
rompp c
m
a
p
r
eading
commit
|
commitdiff
|
tree
2010-02-04
Berk H
e
ss
removed commente
d
out code in p
d
b2top
commit
|
commitdiff
|
tree
2010-02-04
B
e
rk
H
ess
made V
V
bu
f
st
a
te reallocati
o
n cle
a
ner
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fgets2 now g
e
ner
a
tes a fatal err
o
r w
h
e
n
a line is longer
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk H
e
ss
made a
f
atal error m
e
ssage on the
.
vsd
database more
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fixed b
u
g in previous commit of
pdb2top
.
c
commit
|
commitdiff
|
tree
2010-02-03
B
erk Hess
Removed FF
.
dat
commit
|
commitdiff
|
tree
2010-02-03
B
e
rk
H
ess
upda
t
ed Gromos
c-termini
d
a
tabases fo
r
pdb2gmx changes
commit
|
commitdiff
|
tree
2010-02-03
B
erk
Hess
f
ix
e
d
r
eplace and
a
dd iss
u
es in p
d
b2gmx termini pr
o
cess
i
ng
commit
|
commitdiff
|
tree
2010-02-03
Berk H
e
ss
renamed ga2la_home to ga2la_get_home, added ga2la
_
is
_
home
commit
|
commitdiff
|
tree
2010-02-02
Berk Hes
s
fix
e
d i
n
c
o
rrect water H type
i
n gm
x
spc
.
itp spce
.
it
p
.
.
.
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fixe
d
bug in pdb2
g
mx tdb delete processing
commit
|
commitdiff
|
tree
2010-02-02
Berk He
s
s
fixe
d
cr
a
sh
with
vsit
e
s an
d
P
D
commit
|
commitdiff
|
tree
2010-02-02
B
erk Hess
fix
e
d cr
a
sh w
i
th vsites and PD
commit
|
commitdiff
|
tree
2010-02-02
Berk
Hes
s
fixed segv i
n
bcast_state wi
t
h etc=v-re
s
cal
e
an
d
particle
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Be
r
k Hes
s
TE
R
entr
i
es in pdb
file
now get transl
a
ted into chain
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk Hess
the c-ter
m
ini
d
atabases can now retain OXT instea
d
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk Hess
p
d
b2
g
mx can now rename and delete atoms fo
r
m the inp
u
t
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
Berk Hess
c
h
a
n
ged mdrun option
-reseth
m
axh to -resethway a
n
d
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
B
er
k
Hess
resolved
incorrect s
y
m
tab stri
n
g free in pdb2gmx
commit
|
commitdiff
|
tree
2010-01-28
Berk H
e
ss
i
m
plemented force field at
o
m re
n
a
m
ing files for pdb2gmx
commit
|
commitdiff
|
tree
2010-01-28
Berk
H
ess
a
d
ded hidd
e
n
option -resethmaxh to mdrun
commit
|
commitdiff
|
tree
2010-01-28
Berk
Hess
pdb2gmx now c
h
ecks for the existence
of t
h
e water
model
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
rena
m
e
d libfn f
u
nction to gmxlibfn
commit
|
commitdiff
|
tree
2010-01-28
B
e
rk H
e
ss
pdb2gmx
now writes t
h
e relative p
a
th to
.
top when
the
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
gmxcpp is now
a
b
l
e to process
#
inc
l
u
de dir/f
i
l
e where
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk
H
ess
M
ade pdb2
g
m
x
p
rint relati
v
e p
a
ths
for f
f
files when
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Be
r
k Hess
fixed atomprop warning being issued natom
s
times
commit
|
commitdiff
|
tree
2010-01-27
B
e
rk H
e
ss
Removed two
files in sh
a
re/top a
c
cidentally r
e
v
i
ved
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
M
ade
i
ons
.
itp
i
nclude ions
.
i
t
p from the force field
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Moved
a
ll t
h
e ion model
f
i
les
to the force
field s
u
b
d
irectori
e
s
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Moved all the wa
t
er
m
ode
l
files to the
f
o
rc
e
f
ield
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk He
s
s
moved a
l
l f
o
rce field files, except water a
n
d ion
models
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
pdb
2
gmx now detects
a
n
d reads f
o
rce
fie
l
d
f
i
l
es f
r
om
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hes
s
fixed two bugs introdu
c
ed in the pr
e
vio
u
s com
m
it of
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
B
erk
Hess
fix
e
d particl
e
decomposition P-LINCS
set
u
p
commit
|
commitdiff
|
tree
2010-01-26
Berk Hes
s
renamed autocorr -fft opti
o
n to -fttcorr
commit
|
commitdiff
|
tree
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