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t_atoms_set_resinfo now sets rtp to NULL
2010-04-06
Berk Hess
t
_
atoms_
s
et_re
s
info
n
ow sets rtp to NULL
commit
|
commitdiff
|
tree
2010-04-06
Berk Hess
corrected
p
db2g
m
x rtp pr
i
nt condit
i
onal
commit
|
commitdiff
|
tree
2010-04-01
Berk H
e
s
s
added check for NM
a
n
d constrai
n
ts
commit
|
commitdiff
|
tree
2010-03-30
Berk Hess
deprecated the Enca
d
force field
commit
|
commitdiff
|
tree
2010-03-30
Berk Hess
pdb2
g
mx now sorts the forc
e
fiel
d
alphab
e
tically
commit
|
commitdiff
|
tree
2010-03-30
Ber
k
Hess
pdb2gmx
now
also
keeps
the residue na
m
es CYS, HEM and HI
S
commit
|
commitdiff
|
tree
2010-03-24
Ber
k
Hes
s
made g_dist work
w
i
th gro
u
p
s
o
f a single
vs
i
te
commit
|
commitdiff
|
tree
2010-03-23
Berk
H
ess
f
ixed some val
g
rind w
a
rnings
commit
|
commitdiff
|
tree
2010-03-12
Berk Hess
fixed non terminated resname i
n
pdb
2
gmx
commit
|
commitdiff
|
tree
2010-03-11
B
erk Hess
c
l
arified checkpoint
check
s
um mismatch
m
essages
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
Mer
g
e branch 'master' of git@
g
it
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-03-11
Be
r
k Hess
added
m
issing includ
e
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
s
h
ortened t
o
o lon
g
energ
y
names in md
.
l
og
commit
|
commitdiff
|
tree
2010-03-10
Berk
H
es
s
fixed segv with NH and pd
commit
|
commitdiff
|
tree
2010-03-10
Berk Hess
f
i
xe
d
hint i
n
p
d
b2gmx warning
commit
|
commitdiff
|
tree
2010-03-09
B
e
r
k
Hes
s
a
d
d
e
d checks
u
ms for mdrun xvg output
f
iles
commit
|
commitdiff
|
tree
2010-03-09
Berk Hess
fixed g_dipole
a
averag
i
ng descripti
o
ns
commit
|
commitdiff
|
tree
2010-03-09
Berk H
e
s
s
minor fixes for last checkpoint update
commit
|
commitdiff
|
tree
2010-03-08
Berk Hess
made mdrun file appending default and added c
h
ecks
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
Berk H
e
s
s
ad
d
ed
gmx_fatal_collectiv
e
and removed
gmx_
f
atal
.
h
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
Berk
H
e
ss
genbox ca
n
now insert m
u
lti-residue mol
e
cules
commit
|
commitdiff
|
tree
2010-03-05
Berk Hess
fix
e
d bug in const
r
aints with DD
,
vacuum and nc=2
commit
|
commitdiff
|
tree
2010-03-04
Berk Hess
g
roup
e
d VV condition
a
l
s
into one c
o
nditional
commit
|
commitdiff
|
tree
2010-03-04
Berk
H
ess
fixed me
m
ory corruption wi
t
h DD, twin-range and con
s
traints
.
.
.
commit
|
commitdiff
|
tree
2010-03-02
Berk Hess
ad
d
ed opt
i
on to in
i
t_warni
n
g to
turn all
w
arnin
g
s into
.
.
.
commit
|
commitdiff
|
tree
2010-03-02
B
erk Hess
m
o
ved all global variables for input f
i
le checkin
g
.
.
.
commit
|
commitdiff
|
tree
2010-03-01
Berk Hes
s
split
o
ff
w
arninp
.
c wit
h
inp
u
t
re
a
din
g
wa
r
ning rou
t
ines
.
.
.
commit
|
commitdiff
|
tree
2010-03-01
Berk Hess
a
d
ded
char
g
e g
r
o
up size check to grom
p
p
commit
|
commitdiff
|
tree
2010-03-01
Berk Hess
spl
i
t off c
h
argegro
u
p
.
c
f
r
o
m
pbc
.
c
a
nd tpi
.
c
f
rom minim
i
z
e
.
c
commit
|
commitdiff
|
tree
2010-03-01
Berk Hess
cor
r
e
c
ted
n
r
df of
f
rozen sett
l
e
d
molecules
commit
|
commitdiff
|
tree
2010-02-25
Berk H
e
s
s
ano
t
her prec
i
s
i
o
n correction for g_
b
ar
commit
|
commitdiff
|
tree
2010-02-25
B
erk Hess
corrected
the precision o
f
the g_bar output
commit
|
commitdiff
|
tree
2010-02-24
Berk
Hess
fix
e
d pull co
n
straint
memor
y
e
r
ro
r
causing always 100
.
.
.
commit
|
commitdiff
|
tree
2010-02-24
Berk H
e
ss
f
ixed
i
nc
o
rrect wa
l
lcyc
l
e cou
n
t fo
r
update
commit
|
commitdiff
|
tree
2010-02-24
Berk Hes
s
fixed checkpoints not b
e
i
ng w
r
itt
e
n
commit
|
commitdiff
|
tree
2010-02-22
Berk Hess
g_bar n
o
w takes correl
a
tio
n
s al
o
ng la
m
bda into
a
ccount
.
.
.
commit
|
commitdiff
|
tree
2010-02-22
Berk Hess
added slope print for
g_energy
-
s
u
m
commit
|
commitdiff
|
tree
2010-02-22
Berk Hess
c
o
rrec
t
ed NH
vari
a
bles wh
e
n rea
d
ing old tp
x
and
c
pt
.
.
.
commit
|
commitdiff
|
tree
2010-02-17
Berk Hess
some clea
n
-up in the
V
V code in d
o
_md and
fixed the
.
.
.
commit
|
commitdiff
|
tree
2010-02-17
Berk H
e
ss
synchronized checkpoi
n
ting and t
e
rmination with mdr
u
n
.
.
.
commit
|
commitdiff
|
tree
2010-02-16
Berk Hess
fixed a ty
p
o in an err
o
r
message
commit
|
commitdiff
|
tree
2010-02-16
Ber
k
Hess
mdrun n
o
w also checks -
n
pm
e
wit
h
non-paralle
l
compilatio
n
commit
|
commitdiff
|
tree
2010-02-16
Ber
k
Hess
add
e
d check for
mdrun -
d
d and -npme without paralle
l
.
.
.
commit
|
commitdiff
|
tree
2010-02-16
Berk Hess
f
ixed global signaling with VV
commit
|
commitdiff
|
tree
2010-02-15
Berk Hess
collected all
t
he mdrun para
l
lel sign
a
ls into one data
.
.
.
commit
|
commitdiff
|
tree
2010-02-15
Berk Hes
s
fixed de
a
dlocks du
r
ing checkpointing
a
nd ter
m
ination
commit
|
commitdiff
|
tree
2010-02-15
B
erk Hess
m
ade mdr
u
n npm
e
guessing work mo
r
e co
n
siste
n
tl
y
commit
|
commitdiff
|
tree
2010-02-15
B
er
k
Hes
s
fixed
o
utput size es
t
imates
for ener
g
y and dhdl fil
e
s
commit
|
commitdiff
|
tree
2010-02-15
Berk Hess
made read_x
v
g ignore a last non newline terminated
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
Berk
Hess
fixed
p
o
ssible mdrun repe
t
itive war
n
in
g
print with
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
Berk Hess
fi
x
e
d t
e
mperature issue i
n
tr
o
duced in the
l
ast commit
commit
|
commitdiff
|
tree
2010-02-11
Berk
H
ess
made
g
eni
o
n operate on the l
a
st sol
v
ent entry in top
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
replaced the gr
e
ek xvg symbol
escape sequ
e
nc
e
s in
gmxl
i
b
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
mad
e
g_bar rea
d
the temperature
for
t
h
e
dhdl
.
xvg files
commit
|
commitdiff
|
tree
2010-02-10
Berk H
e
ss
change
d
-x
v
gr bool
o
ption t
o
-xvg
e
n
um xmgrace/
x
mgr
.
.
.
commit
|
commitdiff
|
tree
2010-02-09
B
e
rk
Hess
f
i
x
e
d inc
o
rrect virial when n
s
tcalcener
g
y>0
and epc=no
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
changed g_energy -aver
to print the averag
e
i
so the sum
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
fix
e
d
drift in g
_
energy
,
broke a
few commits ago
commit
|
commitdiff
|
tree
2010-02-08
B
e
rk
Hess
introduced STEPSTRSIZE fo
r
print
i
ng gmx_lar
g
e_
i
nt_
t
commit
|
commitdiff
|
tree
2010-02-08
Berk H
e
ss
changed g_ener
g
y and g
_
bar error estimat
i
on to average
.
.
.
commit
|
commitdiff
|
tree
2010-02-05
Berk Hess
cle
a
n
e
d up the g_energy en
e
rgy
stor
a
ge
and added
e
r
ror
.
.
.
commit
|
commitdiff
|
tree
2010-02-04
B
erk Hess
a
d
ded unit f
o
r
g_energy -s
u
m
commit
|
commitdiff
|
tree
2010-02-04
Berk Hess
added
m
i
ssing
i
nclude
commit
|
commitdiff
|
tree
2010-02-04
Berk
H
e
s
s
made i/
o
e
rror checking in
gm
x
cpp
st
r
icter
commit
|
commitdiff
|
tree
2010-02-04
Be
r
k Hess
fixed
a
m
emo
r
y l
e
a
k
i
n grompp
c
ma
p
reading
commit
|
commitdiff
|
tree
2010-02-04
Berk Hess
removed comment
e
d out code in pdb2
t
op
commit
|
commitdiff
|
tree
2010-02-04
B
erk He
s
s
made VV bu
f
stat
e
r
e
allocation cleaner
commit
|
commitdiff
|
tree
2010-02-03
Berk
H
ess
fge
t
s2 now gener
a
tes a fat
a
l error when
a
line is
lon
g
er
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk
H
e
ss
made
a
f
atal error messag
e
on t
h
e
.
vsd
d
atabas
e
mo
r
e
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
B
e
rk Hess
f
ixed bu
g
in previous c
o
mmit of p
d
b2top
.
c
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
Removed FF
.
dat
commit
|
commitdiff
|
tree
2010-02-03
Berk Hes
s
updated Gromos c-termi
n
i da
t
a
bases for
p
db2gmx
c
h
anges
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fixed re
p
lace and a
d
d i
s
sues in pdb2gmx termini proce
s
sing
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
renamed ga2la_h
o
me
t
o ga2la_get_ho
m
e, added g
a
2la_i
s
_home
commit
|
commitdiff
|
tree
2010-02-02
Ber
k
Hess
fi
x
e
d
i
ncorre
c
t wa
t
er H type
in gmx s
p
c
.
itp
spce
.
itp
.
.
.
commit
|
commitdiff
|
tree
2010-02-02
Ber
k
Hess
fixed bug i
n
p
d
b
2
gmx tdb dele
t
e processi
n
g
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fixe
d
c
rash
w
ith vsites
and
PD
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fixed crash with v
s
i
t
es
and
PD
commit
|
commitdiff
|
tree
2010-02-02
Ber
k
He
s
s
fixed segv in bcast_state with etc=v-r
e
s
c
ale and part
i
c
le
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Ber
k
Hess
TE
R
entries
i
n pdb file now get trans
l
ated
int
o
c
h
a
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk
Hess
the c-termini databases
c
an now retain
OXT i
n
stead
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Ber
k
Hess
pdb2gmx can now renam
e
and d
e
l
ete atoms form the inpu
t
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
B
erk He
s
s
changed mdrun o
p
tion -
r
esethmaxh to
-resethway and
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
Berk Hess
resolved in
c
orrec
t
symtab string free
i
n
p
db2gmx
commit
|
commitdiff
|
tree
2010-01-28
Berk He
s
s
implemented
f
o
rce field atom renaming
files for
p
db2gmx
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
added hi
d
d
en option -reset
h
m
axh to mdrun
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
pdb2gmx now
c
hecks for
the exi
s
t
e
n
c
e
of the water model
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
B
erk Hess
r
enamed libf
n
f
unction
t
o
g
mxlibfn
commit
|
commitdiff
|
tree
2010-01-28
B
erk Hess
pdb2gmx n
o
w
writes
t
he r
e
lat
i
ve path to
.
top when
the
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
gmxcpp is now
a
b
le to process
#
include
d
ir/f
i
le w
h
ere
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
Made pdb2g
m
x print
relati
v
e
p
a
ths
f
o
r ff f
i
les
when
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk
H
ess
fixed atomprop war
n
i
n
g bein
g
issued nato
m
s times
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Removed two fi
l
e
s
in share/top accidentally revive
d
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Made ions
.
itp i
n
cl
u
de
ions
.
itp
f
rom the fo
r
ce field
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Be
r
k Hess
Move
d
all t
h
e
ion model files t
o
the force fie
l
d
subdirec
t
ories
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Moved all the water mod
e
l files
to the force field
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
moved all force f
i
el
d
f
i
les, except wate
r
and
ion m
o
del
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
pdb2
g
mx now
detects
and r
e
ads force field fil
e
s from
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk He
s
s
f
ixed
t
wo bugs i
n
troduced in the previous c
o
mmit of
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
Berk
H
ess
fixed particle decompositio
n
P-
L
INCS setup
commit
|
commitdiff
|
tree
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