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fixed possible mdrun repetitive warning print with DLB auto
2010-02-12
Berk Hess
fixed po
s
sible mdrun
repetitive warning pr
i
nt
with
.
.
.
commit
|
commitdiff
|
tree
2010-02-12
B
e
rk Hess
f
i
xed
t
em
p
erature issue introduced in the last commit
commit
|
commitdiff
|
tree
2010-02-11
Berk Hess
made genion o
p
erate on the last solvent entry
i
n
top
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Be
r
k Hess
rep
l
aced
t
he
g
reek xvg
s
ymbol escape sequences
i
n gmxlib
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Berk Hess
made g_bar read
t
he te
m
perature f
o
r the dhd
l
.
xvg fi
l
es
commit
|
commitdiff
|
tree
2010-02-10
B
erk Hes
s
chang
e
d -xv
g
r bool optio
n
to -xvg
enu
m
xmgrac
e
/xmgr
.
.
.
commit
|
commitdiff
|
tree
2010-02-09
B
e
rk H
e
ss
fixed incorrect virial whe
n
nst
c
a
lcener
g
y
>
0 and epc=no
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
changed g_energ
y
-aver to print
the average iso the sum
commit
|
commitdiff
|
tree
2010-02-08
Berk He
s
s
fixed drift
i
n
g_energy, broke a few commits ago
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
intr
o
duced STEPS
T
RSIZE f
o
r pr
i
nting gmx_
l
arge
_
int_t
commit
|
commitdiff
|
tree
2010-02-08
Berk Hess
changed
g
_e
n
ergy and g_bar error esti
m
ation to aver
a
g
e
.
.
.
commit
|
commitdiff
|
tree
2010-02-05
Berk Hess
cleaned up the g_
e
ner
g
y energy st
o
r
a
g
e and a
d
ded error
.
.
.
commit
|
commitdiff
|
tree
2010-02-04
Ber
k
Hess
added unit for g
_
energy -sum
commit
|
commitdiff
|
tree
2010-02-04
Berk Hess
added missing
includ
e
commit
|
commitdiff
|
tree
2010-02-04
B
e
rk Hess
ma
d
e i/o
e
r
ror chec
k
in
g
in
g
mx
c
pp stricter
commit
|
commitdiff
|
tree
2010-02-04
Berk Hess
f
i
xe
d
a memo
r
y
leak
i
n grompp cmap
rea
d
ing
commit
|
commitdiff
|
tree
2010-02-04
Berk Hess
removed c
o
m
mented
o
u
t
code in pdb2top
commit
|
commitdiff
|
tree
2010-02-04
B
erk Hess
made VV bufstate r
e
allocation cleaner
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fgets2 now generat
e
s
a fatal error whe
n
a
line is longer
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk
H
es
s
m
ade a
fatal error message on the
.
vsd
database more
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Berk Hes
s
fixed
b
u
g in p
r
evious
commit of pdb2top
.
c
commit
|
commitdiff
|
tree
2010-02-03
Berk H
e
ss
Rem
o
ved FF
.
dat
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
updated Gromos c-termini database
s
f
o
r pdb2gmx changes
commit
|
commitdiff
|
tree
2010-02-03
Berk Hess
fi
x
e
d
replace
an
d
add iss
u
es in p
d
b2gmx termini proce
s
s
ing
commit
|
commitdiff
|
tree
2010-02-03
B
erk Hess
renamed
g
a2la_ho
m
e
t
o g
a
2la_get_home, ad
d
ed ga2la_is_home
commit
|
commitdiff
|
tree
2010-02-02
Berk Hess
fixed
i
n
corr
e
ct water
H type in gmx sp
c
.
it
p
spce
.
itp
.
.
.
commit
|
commitdiff
|
tree
2010-02-02
Berk
H
ess
fixed bug in pd
b
2gmx t
d
b de
l
ete pr
o
cess
i
ng
commit
|
commitdiff
|
tree
2010-02-02
Berk
H
ess
fixed c
r
as
h
w
ith
v
s
it
e
s and PD
commit
|
commitdiff
|
tree
2010-02-01
B
erk
H
ess
T
ER
e
ntries in
p
db
f
ile now get
t
r
a
n
s
late
d
in
t
o chain
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk Hess
the c-termi
n
i databases can now
retain O
X
T i
n
stead
.
.
.
commit
|
commitdiff
|
tree
2010-02-01
Berk Hess
pdb2gmx can now r
e
name an
d
delete
atoms form t
h
e input
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
Berk
H
ess
changed mdrun
opti
o
n -reseth
m
axh to -reseth
w
a
y
and
.
.
.
commit
|
commitdiff
|
tree
2010-01-29
Berk
Hess
resolved i
n
c
o
rrect symtab string f
r
ee in pdb2gmx
commit
|
commitdiff
|
tree
2010-01-28
Berk
H
ess
im
p
leme
n
ted force field atom r
e
na
m
ing files
f
o
r pd
b
2gmx
commit
|
commitdiff
|
tree
2010-01-28
Be
r
k Hess
added hidden option -r
e
sethmaxh to mdr
u
n
commit
|
commitdiff
|
tree
2010-01-28
Be
r
k
Hes
s
pdb2gm
x
now che
c
ks fo
r
the
e
x
i
s
tence of the water m
o
del
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
renamed libfn function to gm
x
libfn
commit
|
commitdiff
|
tree
2010-01-28
Ber
k
He
s
s
pdb2g
m
x no
w
writes th
e
re
l
ative path to
.
top when
t
he
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Berk Hess
gmxcpp is now able to
p
roces
s
#
i
nc
l
ude dir/file w
h
ere
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
B
erk He
s
s
Made pdb2
g
m
x
print
relat
i
ve paths for
ff
f
i
le
s
when
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Be
r
k Hess
f
ixe
d
atomp
r
o
p warning being i
s
sued n
a
tom
s
times
commit
|
commitdiff
|
tree
2010-01-27
Berk
H
ess
Re
m
oved two files i
n
sh
a
re/top accidenta
l
ly revived
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
B
erk He
s
s
Made
i
ons
.
itp inc
l
u
de
ion
s
.
itp from the forc
e
f
i
eld
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
B
erk
H
e
ss
Move
d
a
ll the ion model files to
the
f
orce field
s
ubdir
e
ctories
.
commit
|
commitdiff
|
tree
2010-01-27
Berk He
s
s
Move
d
all
t
he water model files to the fo
r
ce
f
ie
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk H
e
ss
moved all force fie
l
d
f
iles
,
except water
and
i
o
n models
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
B
e
r
k
Hess
pdb2gmx now de
t
ects and reads
force f
i
el
d
fi
l
e
s
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-01-27
Berk He
s
s
fixed
two bugs in
t
rodu
c
e
d
in
the previous
c
o
m
m
it of
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
Berk Hess
fixed partic
l
e decomposit
i
on P-
L
INCS setup
commit
|
commitdiff
|
tree
2010-01-26
Berk Hess
ren
a
med autocorr
-
fft option t
o
-fttc
o
r
r
commit
|
commitdiff
|
tree
2010-01-26
Berk
H
ess
a
d
ded pull_
g
eome
t
ry=directi
o
n_periodic to
m
dp_opt
.
html
commit
|
commitdiff
|
tree
2010-01-26
Ber
k
Hess
s
h
o
rtened too long names
f
o
r
GB bo
n
deds
commit
|
commitdiff
|
tree
2010-01-26
Berk Hess
fixed so
m
e comments
in forcerec
.
c
commit
|
commitdiff
|
tree
2010-01-26
Berk Hess
made mdru
n
-pforce also
catch NAN forces
commit
|
commitdiff
|
tree
2010-01-26
Berk Hess
ad
d
ed mis
s
i
ng nblist initializations
commit
|
commitdiff
|
tree
2010-01-25
Berk Hess
added
m
issi
n
g
cmap_grid copy in dd_init
_
local_t
o
p
commit
|
commitdiff
|
tree
2010-01-25
Berk
H
ess
f
ixed segv
w
ith i
n
tegrat
o
r sd2
commit
|
commitdiff
|
tree
2010-01-25
Berk
H
ess
changed -v verb
o
s
ity option
to -verb to avo
i
d confict
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Berk Hes
s
added warni
n
g for using full electrostatics without
.
.
.
commit
|
commitdiff
|
tree
2010-01-21
Berk Hess
made g_bar use a toleran
c
e
f
or
lambda
val
u
e
c
ompari
s
on
commit
|
commitdiff
|
tree
2010-01-21
Berk Hes
s
correct
e
d the descr
i
ptio
n
of gmx
_
within_tol
commit
|
commitdiff
|
tree
2010-01-19
Berk Hess
fix
e
d
residue renumbering for
m
ulti-
r
esidue
m
olecu
l
es
commit
|
commitdiff
|
tree
2010-01-19
Berk
H
ess
added -group option to g_min
d
is
t
commit
|
commitdiff
|
tree
2010-01-19
B
erk Hess
fixed
i
ncorre
c
t
residue renumbering
in t_a
t
oms rea
d
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Berk Hess
switched off automat
i
c DD decompositi
o
n in z with ewald_geom=
3
dc
commit
|
commitdiff
|
tree
2010-01-18
Berk Hess
f
i
xed in
c
o
mplete
(
not
in
c
orrect) eneconv
c
o
ncatenation
commit
|
commitdiff
|
tree
2010-01-15
Be
r
k
H
ess
imple
m
ented
p
db
2
gmx residue ren
a
ming
commit
|
commitdiff
|
tree
2010-01-14
Berk
Hess
removed superfluou
s
dgdl from open_
d
hdl
print
commit
|
commitdiff
|
tree
2010-01-14
B
e
rk Hess
re
m
ove
d
t
h
e
cgnr opt
i
o
n for
replace in the term
i
ni
.
.
.
commit
|
commitdiff
|
tree
2010-01-14
Berk
Hess
c
gn
r
is
n
ow
pr
o
p
erly read in ter d
b
replac
e
e
n
tr
i
es
commit
|
commitdiff
|
tree
2010-01-14
B
erk Hess
fixed pd
b
2gmx -p dir/topol
.
top top include statements
commit
|
commitdiff
|
tree
2010-01-12
Berk Hess
fixed parallel md
r
un termination
a
nd nstlist=-1
commit
|
commitdiff
|
tree
2010-01-12
Berk Hess
made check
p
o
i
ting work again in parallel
commit
|
commitdiff
|
tree
2010-01-11
Berk Hess
m
a
de molecules whole
i
n confo
u
t afte
r
EM
commit
|
commitdiff
|
tree
2010-01-11
Berk Hes
s
made separate arrays for NH pressur
e
variab
l
es
commit
|
commitdiff
|
tree
2010-01-11
Berk Hess
fixed
c
o
mpiler warning
commit
|
commitdiff
|
tree
2010-01-08
Be
r
k Hess
fi
x
ed hang in compute_globals
commit
|
commitdiff
|
tree
2010-01-08
Berk
Hess
made particle decom
p
ostion work again wi
t
h l
i
ncs on
.
.
.
commit
|
commitdiff
|
tree
2010-01-08
Berk Hess
made g
r
aph
.
edge a s
i
ngle array
commit
|
commitdiff
|
tree
2010-01-05
Berk Hes
s
add extra
o
u
tput fi
l
e t
o
g
_
bar
commit
|
commitdiff
|
tree
2010-01-05
Be
r
k Hess
split md
.
c into md
.
c a
n
d
runne
r
.
c
commit
|
commitdiff
|
tree
2010-01-05
Berk Hess
s
et nnhchains to 0
when n
o
t using NH
commit
|
commitdiff
|
tree
2010-01-05
Berk
Hess
re
n
am
e
d r
e
s
t
r
.
bond to rest
r
aint pot
.
commit
|
commitdiff
|
tree
2010-01-04
B
e
r
k
Hes
s
removed NH chains no
t
e when n
o
t using
N
H
commit
|
commitdiff
|
tree
2010-01-04
Berk Hess
impl
e
me
n
t
e
d
r
estr
a
int bond
s
commit
|
commitdiff
|
tree
2010-01-04
B
er
k
Hess
fixed t
h
e s
o
rting of 1-4 FE intera
c
t
i
ons for fo
r
eign
.
.
.
commit
|
commitdiff
|
tree
2009-12-17
Berk Hess
fixed typos in
t
he
g_msd des
c
r
i
ption
commit
|
commitdiff
|
tree
2009-12-17
Berk He
s
s
Merge bra
n
ch '
m
aster' of git@git
.
g
r
omac
s
.
org:gr
o
m
a
cs
commit
|
commitdiff
|
tree
2009-12-17
Berk Hess
c
orrec
t
ed
t
h
e g_
m
s
d
descript
i
on
commit
|
commitdiff
|
tree
2009-12-15
Berk Hess
fixed the
c
y
cle count
e
r
n
for the PME
s
u
b
division
commit
|
commitdiff
|
tree
2009-12-15
Berk
Hess
added
P
ME sub
d
ivision to cycle counters
commit
|
commitdiff
|
tree
2009-12-15
Berk H
e
s
s
added PME subdivi
s
i
on t
o
cycle coun
t
ers
commit
|
commitdiff
|
tree
2009-12-09
Berk H
e
ss
fixed
g_r
d
f -s -xy hanging
commit
|
commitdiff
|
tree
2009-12-07
Berk
H
ess
added new in
c
lude files to inclu
d
e
/
Makefi
l
e
.
am
commit
|
commitdiff
|
tree
2009-12-02
B
e
rk Hess
fix
e
d incorrect g_ba
r
check for
missin
g
la
m
b
da
v
alues
commit
|
commitdiff
|
tree
2009-12-02
B
erk Hess
fixed g
a
2la in
d
ex for
empt
y
DD cells
commit
|
commitdiff
|
tree
2009-11-19
B
e
rk Hess
Merge bra
n
ch '
m
a
ster' of git@g
i
t
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-11-19
B
e
rk Hess
fixed the g_rmsf -res option
commit
|
commitdiff
|
tree
2009-11-11
Berk Hess
fi
x
e
d
compiler warning
commit
|
commitdiff
|
tree
2009-11-11
Berk Hess
added exclusio
n
suppor
t
for cg-cg loops
commit
|
commitdiff
|
tree
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