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corrected pdb2gmx rtp print conditional
2010-04-06
Ber
k
Hess
co
r
r
e
cted pdb2gmx rtp print conditional
commit
|
commitdiff
|
tree
2010-04-01
Berk H
e
ss
added
check f
o
r NM and cons
t
raints
commit
|
commitdiff
|
tree
2010-03-30
Berk Hess
depr
e
ca
t
ed the Encad force fie
l
d
commit
|
commitdiff
|
tree
2010-03-30
Berk H
e
ss
p
d
b2
g
mx now sor
t
s
the
force
f
ie
l
d alphabetical
l
y
commit
|
commitdiff
|
tree
2010-03-30
Berk Hess
pdb2g
m
x
now also keep
s
the residue n
a
mes CYS, HEM and HIS
commit
|
commitdiff
|
tree
2010-03-24
Berk Hess
m
ade g_dist wo
r
k with groups of a s
i
ngl
e
vsite
commit
|
commitdiff
|
tree
2010-03-23
Be
r
k Hess
fixed so
m
e v
a
lgrind
w
arni
n
gs
commit
|
commitdiff
|
tree
2010-03-12
B
e
rk
H
e
ss
f
ixed
n
on t
e
rminated res
n
ame in pdb2gmx
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
c
larified c
h
eckpoint c
h
ec
k
su
m
m
ismatc
h
messa
g
es
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
Merge branch 'm
a
ster
'
of git@git
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
added missin
g
i
n
clud
e
commit
|
commitdiff
|
tree
2010-03-11
Berk Hess
sho
r
tened too long energy n
a
m
e
s
in
m
d
.
log
commit
|
commitdiff
|
tree
2010-03-10
Ber
k
Hess
f
ixed s
e
gv w
i
th
N
H
an
d
pd
commit
|
commitdiff
|
tree
2010-03-10
B
erk Hess
fi
x
ed hint in pdb2g
m
x warning
commit
|
commitdiff
|
tree
2010-03-09
B
erk Hess
adde
d
c
hecksums for
mdrun x
v
g ou
t
put files
commit
|
commitdiff
|
tree
2010-03-09
Berk Hess
fi
x
ed g_dipolea aver
a
ging de
s
cript
i
ons
commit
|
commitdiff
|
tree
2010-03-09
Ber
k
Hess
minor fixes f
o
r
last c
h
e
c
k
poi
n
t update
commit
|
commitdiff
|
tree
2010-03-08
Berk Hess
mad
e
mdrun file appending
de
f
ault
a
n
d
added che
c
ks
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
B
e
r
k He
s
s
added gm
x
_fat
a
l_co
l
l
e
ctiv
e
a
nd
r
emoved
g
mx_fatal
.
h
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
Ber
k
Hess
genbox
can
n
o
w
insert m
u
l
ti-residue molecules
commit
|
commitdiff
|
tree
2010-03-05
Berk Hess
fixed bug in constraints with DD, vacuum and n
c
=2
commit
|
commitdiff
|
tree
2010-03-04
Be
r
k
Hess
grouped VV con
d
itionals
i
nto
one
c
onditional
commit
|
commitdiff
|
tree
2010-03-04
B
erk Hess
fi
x
e
d
memory co
r
ruption with
D
D
, twin-ran
g
e and
constrai
n
ts
.
.
.
commit
|
commitdiff
|
tree
2010-03-02
B
e
rk Hess
added option to ini
t
_
warning
to turn all warn
i
ngs
into
.
.
.
commit
|
commitdiff
|
tree
2010-03-02
Ber
k
Hess
mov
e
d al
l
global varia
b
le
s
for i
n
put file chec
k
ing
.
.
.
commit
|
commitdiff
|
tree
2010-03-01
B
erk Hess
spl
i
t
off warninp
.
c with input re
a
ding
w
arnin
g
routines
.
.
.
commit
|
commitdiff
|
tree
2010-03-01
Berk Hess
added charge grou
p
siz
e
check to grompp
commit
|
commitdiff
|
tree
2010-03-01
B
erk Hess
spli
t
o
ff cha
r
gegroup
.
c
from pbc
.
c and tpi
.
c from min
i
miz
e
.
c
commit
|
commitdiff
|
tree
2010-03-01
B
erk
Hes
s
corrected
n
rdf of fr
o
zen
s
ettled
m
olecules
commit
|
commitdiff
|
tree
2010-02-25
Berk Hess
an
o
ther precision corr
e
c
t
ion
for g_
b
ar
commit
|
commitdiff
|
tree
2010-02-25
Berk Hess
co
r
rected
the
precis
i
on of the g_bar o
u
tput
commit
|
commitdiff
|
tree
2010-02-24
Berk He
s
s
f
i
x
e
d pul
l
constrai
n
t memo
r
y
e
rror causing alw
a
ys 100
.
.
.
commit
|
commitdiff
|
tree
2010-02-24
Berk Hess
fixed
i
n
corr
e
ct wallcycle
c
ount for up
d
a
te
commit
|
commitdiff
|
tree
2010-02-24
Berk Hess
fixe
d
c
h
eckpoints not being
w
ritten
commit
|
commitdiff
|
tree
2010-02-22
Berk Hess
g_bar
now takes correla
t
ions along lamb
d
a in
t
o account
.
.
.
commit
|
commitdiff
|
tree
2010-02-22
Berk Hes
s
add
e
d slope print for g_energy -sum
commit
|
commitdiff
|
tree
2010-02-22
B
erk
H
ess
corrected
NH va
r
iables
w
hen re
a
di
n
g old tpx and cpt
.
.
.
commit
|
commitdiff
|
tree
2010-02-17
Berk Hess
s
o
me clean-up in
t
he VV code
i
n do_md an
d
fixed the
.
.
.
commit
|
commitdiff
|
tree
2010-02-17
Berk Hess
sync
h
ronize
d
check
p
o
inti
n
g and t
e
r
m
inat
i
o
n with mdru
n
.
.
.
commit
|
commitdiff
|
tree
2010-02-16
B
erk Hess
fixed
a t
y
p
o
in an e
r
ror messag
e
commit
|
commitdiff
|
tree
2010-02-16
Berk He
s
s
m
d
run now also checks -npme
with non-p
a
rallel compilation
commit
|
commitdiff
|
tree
2010-02-16
Ber
k
Hess
added c
h
e
c
k
for
m
d
r
u
n
-dd and -npme without parallel
.
.
.
commit
|
commitdiff
|
tree
2010-02-16
B
e
r
k
H
e
s
s
fi
x
ed glo
b
a
l
sign
a
ling with
VV
commit
|
commitdiff
|
tree
2010-02-15
Ber
k
Hess
coll
e
cted all t
h
e mdru
n
paral
l
el
s
ignals into o
n
e data
.
.
.
commit
|
commitdiff
|
tree
2010-02-15
Berk
He
s
s
fixed deadlocks during checkpointing and termination
commit
|
commitdiff
|
tree
2010-02-15
Be
r
k Hess
m
ade mdrun npme gu
e
ssing work more consi
s
tently
commit
|
commitdiff
|
tree
2010-02-15
Berk Hess
fixed output siz
e
estimates fo
r
ener
g
y a
n
d d
h
dl files
commit
|
commitdiff
|
tree
2010-02-15
Berk Hess
m
ade rea
d
_xvg igno
r
e a
l
as
t
non
n
ewlin
e
terminate
d
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
Berk Hess
fixed
p
ossible mdrun
r
e
petitive warni
n
g print with
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
Be
r
k
H
e
ss
fixed tem
p
erature issue
introduced in the
l
a
s
t commit
commit
|
commitdiff
|
tree
2010-02-11
Berk Hess
m
a
de genion operate
o
n th
e
last s
o
lvent entry
in top
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Be
r
k Hess
replaced the gree
k
xvg s
y
mbol escape sequen
c
e
s in gmxlib
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
made g_
b
ar read the
t
e
m
perature
for the
dhdl
.
xvg
files
commit
|
commitdiff
|
tree
2010-02-10
Berk
Hess
c
hanged -xvgr bool option to
-
x
vg
enum
xmgrace/xmgr
.
.
.
commit
|
commitdiff
|
tree
2010-02-09
Ber
k
Hess
fixed incorr
e
ct v
i
ri
a
l when nst
c
alcenergy>0 and ep
c
=n
o
commit
|
commitdiff
|
tree
2010-02-08
Berk Hes
s
changed g_ener
g
y -av
e
r to print
t
he a
v
erage iso the sum
commit
|
commitdiff
|
tree
2010-02-08
Berk Hes
s
f
ixe
d
drift i
n
g_energy, broke a few commits
ago
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
i
nt
r
oduced STE
P
S
T
RSI
Z
E fo
r
printin
g
gmx_large_int_t
commit
|
commitdiff
|
tree
2010-02-08
Ber
k
H
ess
changed g_energ
y
and
g
_bar error est
i
m
ation to average
.
.
.
commit
|
commitdiff
|
tree
2010-02-05
Berk He
s
s
cleaned u
p
the
g
_energy e
n
ergy stora
g
e and added error
.
.
.
commit
|
commitdiff
|
tree
2010-02-04
Berk H
e
ss
adde
d
unit f
o
r g_energy -sum
commit
|
commitdiff
|
tree
2010-02-04
Berk H
e
ss
added missing
i
ncl
u
d
e
commit
|
commitdiff
|
tree
2010-02-04
Berk
Hess
made i/o error ch
e
cking in
g
mxcpp stric
t
er
commit
|
commitdiff
|
tree
2010-02-04
Ber
k
Hess
f
i
xed a
me
m
ory leak in grompp cmap
reading
commit
|
commitdiff
|
tree
2010-02-04
Ber
k
He
s
s
removed co
m
mented out cod
e
in
p
d
b
2
t
op
commit
|
commitdiff
|
tree
2010-02-04
Berk He
s
s
made VV bufstate reallocation clea
n
er
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fg
e
ts2 now generates a fatal
error when
a
li
n
e is longer
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk H
e
ss
made a
f
atal error message
on the
.
vsd database
more
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fixed
b
ug
in previo
u
s commit
o
f pdb2top
.
c
commit
|
commitdiff
|
tree
2010-02-03
Berk He
s
s
Remo
v
e
d FF
.
da
t
commit
|
commitdiff
|
tree
2010-02-03
B
e
rk Hess
u
p
da
t
e
d Gromos c-termini databases for pdb2gmx
c
han
g
e
s
commit
|
commitdiff
|
tree
2010-02-03
B
e
rk Hess
fixed r
e
place and add iss
u
es i
n
p
d
b2gmx te
r
mini
processing
commit
|
commitdiff
|
tree
2010-02-03
B
e
rk
Hess
re
n
amed ga2la_h
o
me to ga2la_get_home, added ga2la_is_home
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
f
i
x
e
d in
c
orrec
t
water
H
type i
n
gmx spc
.
i
t
p sp
c
e
.
it
p
.
.
.
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fi
x
e
d
bug in pdb2gmx
tdb delete p
r
ocessing
commit
|
commitdiff
|
tree
2010-02-02
B
erk Hess
fixed cr
a
sh with vsites and PD
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fixed crash
w
ith
vs
i
tes a
n
d PD
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fixed segv in bcast_
s
tate
with e
t
c=v-r
e
s
c
ale and particle
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk Hess
T
E
R entries
in pdb fil
e
now get tr
a
nslated in
t
o cha
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk
H
e
ss
the c-te
r
mini databases can now r
e
tain OXT
i
nst
e
ad
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk
He
s
s
pdb2g
m
x can now rename and delete atoms form the i
n
put
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
Berk Hess
chan
g
ed mdrun option -reseth
m
axh to -resethwa
y
a
nd
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
B
erk Hess
resolve
d
incorrect symtab s
t
ring free in pdb
2
gmx
commit
|
commitdiff
|
tree
2010-01-28
Be
r
k Hess
impl
e
mented force field at
o
m
r
enaming files for pdb2
g
mx
commit
|
commitdiff
|
tree
2010-01-28
Berk
H
es
s
added hi
d
den o
p
t
i
on -re
s
et
h
maxh to md
r
un
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
pdb2gm
x
now c
h
e
c
ks for the
e
xistence of the
w
a
t
e
r mod
e
l
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
renamed libfn functi
o
n to gmxlibfn
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
p
db2gmx no
w
wr
i
tes t
h
e relative p
a
th to
.
top
w
hen the
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk He
s
s
gmxcpp is
n
ow able to pr
o
cess #include dir/file where
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk
Hess
Made pdb2g
m
x pr
i
nt
r
el
a
tive paths for ff fil
e
s w
h
en
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk
Hess
fixed atompr
o
p wa
r
ning being issued natoms t
i
mes
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Re
m
ov
e
d
two files in s
h
are/top acciden
t
ally
revived
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Mad
e
ions
.
itp include ions
.
itp
fro
m
the f
o
rce
f
i
e
ld
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk
H
e
ss
Moved all the ion model fil
e
s
to the force field
s
ubdirectories
.
commit
|
commitdiff
|
tree
2010-01-27
Berk Hess
Mo
v
ed all the water model
fil
e
s
to the force field
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
B
erk Hess
moved all
f
o
rce
fie
l
d files,
e
xcept water and ion models
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk He
s
s
pdb2gmx now detects
a
nd r
e
ads force fie
l
d f
i
le
s
from
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
B
e
rk Hess
fixed t
w
o bugs intro
d
uced in the pre
v
ious
c
ommit
o
f
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
Be
r
k Hess
fixed particle
d
ecompo
s
it
i
on P-LINC
S
s
e
t
up
commit
|
commitdiff
|
tree
2010-01-26
Berk Hess
r
e
named a
u
tocorr -fft o
p
tion to -fttcorr
commit
|
commitdiff
|
tree
next