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added some comment to group grompp assignment options
2010-08-18
Berk Hess
added so
m
e comment
t
o
gr
o
u
p
g
ro
m
p
p assignment
o
p
tions
commit
|
commitdiff
|
tree
2010-08-18
B
e
rk Hess
added g
r
oup comparison to gmxcheck and print groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk Hes
s
fi
x
ed possible
p
athe stri
n
g buffer overflow
in
get_libdir
commit
|
commitdiff
|
tree
2010-08-17
Berk H
e
ss
added functio
n
r
escal
e
_veloc
i
ties
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk
H
e
ss
gmx_rmpbc now guesses ePBC again f
o
r
each fr
a
me
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc gets
natoms passed
again, wit
h
out n
a
toms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
B
e
r
k Hess
pu
t
omp pragma's
in fft5
d
.
c betwee
n
ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
added ope
n
m
p
pragma'
s
f
or the
fft5d t
r
a
n
spose routine
s
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
fixed
m
d
run
w
rites tpi
d
ist
.
xvg on all nod
e
s
commit
|
commitdiff
|
tree
2010-08-16
Berk
Hess
fixed segv i
n
mdrun with repli
c
a
e
x
cha
n
g
e
commit
|
commitdiff
|
tree
2010-08-16
Berk Hes
s
fixed fatal error in md
r
un file appendi
n
g with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
gmxcheck now pr
i
n
t
s
rms
d
's
as
%
g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Berk H
e
ss
moved full
pre
c
ision real format definition
to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
Hess
rever
t
ed
th
e
l
a
st, non-cosmetic
change to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hes
s
minor cos
m
etic change
s
i
n pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk
Hes
s
ma
d
e the pd
b
2gmx occupancy warni
n
g more obvious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
f
i
xed i
n
correct pdb2gmx output wi
t
h
m
u
ltipl
e
(alt
l
oc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
removed -merge fr
o
m the pdb2gm
x
manua
l
and c
l
arified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk H
e
ss
fixed bug
t
hat caused
a segv when sn
e
w
f
ailed
commit
|
commitdiff
|
tree
2010-08-10
B
e
rk Hess
removed CYS2 from the
A
mber
r
tp
f
iles
commit
|
commitdiff
|
tree
2010-08-10
B
e
rk
Hess
removed pdb2gmx -c
y
sh hidden option that shou
l
d
h
ave
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk He
s
s
made mdrun -s
e
ppo
t
w
ork with thre
a
d
s
and -seppot no
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
erk Hess
Merge
b
ranch 'release-4-5-
p
at
c
hes' of
g
it@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk H
e
ss
corrected the (irrelevant) defaul
t
i
r
-
>gb_dielectric_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
added -pbc option to g_traj
commit
|
commitdiff
|
tree
2010-08-05
B
er
k
H
e
ss
read
i
np,
used for
e
.
g
.
mdp
,
no longer use
s
gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
B
e
r
k Hess
fixed gmx_rmpbc un
d
o
ing the shifting when x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
s
c_sigma now also sets t
h
e minimum value for the sof
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk H
e
s
s
make_ndx
n
ow allows nearly
all characters in a
t
om and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
r
k
Hess
gmxche
c
k n
o
w c
o
mpares
t
e
r
m
s
by name matching
commit
|
commitdiff
|
tree
2010-08-04
B
e
r
k H
e
ss
remove
d
commrec->nthread
s
from FAHCORE cod
e
commit
|
commitdiff
|
tree
2010-08-04
Be
r
k Hess
gmxc
h
e
c
k now
u
si
n
g the diagon
a
l fo
r
re
l
ative tole
r
ance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
e
r
k He
s
s
fix
e
d g
_
energy manual formatting issues
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
grompp autom
a
ti
c
ns
t
c
alcenergy set
t
in
g
now
t
ak
e
s
small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
added full precision option to g_tr
a
j
a
nd
reformatted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk
Hess
fixed PME communicati
o
n
r
ange
when first DD dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
B
e
r
k Hess
made vrescale and Be
r
endsen tco
u
ple work with VV, although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk
H
ess
corrected
L
J
on H
of ch
a
rmm t
i
ps3p
commit
|
commitdiff
|
tree
2010-07-29
Ber
k
Hes
s
com
p
let
e
d
pa
r
tial ren
a
me
o
f CYN to C
Y
S
f
o
r
Amber
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
Hess
corrected
t
he Amber aminoacids
.
r
2
b
f
iles
commit
|
commitdiff
|
tree
2010-07-28
Berk H
e
ss
rename
d
pme_maxshift0/1 to
p
m
e_
m
axsh
i
ft_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
repla
c
e
d
t
h
e Cha
r
mm vsit
e
parameter
s
(which were
O
PLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
H
e
ss
co
r
rect
e
d a
v
site parameter
in the amber
f
f's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
c
orrect
e
d Cl at
o
m name in amber ion
s
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
amber ff atomtype
s
change
:
corrected
m
a
s
ses, re
m
ov
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
updat
e
of amber03 am
i
noa
c
ids
.
r
t
p
,
accidental
l
y left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
cor
r
ected
m
i
stakes in a
m
ber
0
3 gb
s
a
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
fixed typo in Make
f
ile
commit
|
commitdiff
|
tree
2010-07-27
Berk He
s
s
moved
f
f
_d
u
m
.
itp
t
o
the gmx
a
nd gromos ff d
i
r
e
ctories
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
co
r
rected
t
he
a
mber vs
i
te parameters
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
adde
d
his to
o
p
ls r2b file
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
made the ff file
nam
i
n
g
of a
m
ber and charmm consisten
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
co
r
recte
d
t
he
a
mber
w
ater model fil
e
s
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PME decomposition
check for inverse DD ord
e
r
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed amber LYP
t
o LYS a
n
d c
h
anged nam
e
s f
o
r wa
t
er
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
re
m
oved HOH f
r
o
m
amber
rn
a
.
hd
b
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
dded
mi
s
sin
g
e
ntries
f
or amber rna
.
h
d
b
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
cle
a
ned up Amber hdb
'
s
a
n
d add
e
d
HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed atom types
f
rom amber99_
?
etc
.
to the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
fi
x
ed PME comm
u
nica
t
ion ra
n
ge
(
no
s
i
l
en
t
err
o
r
s
)
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
emoved building blo
c
k RT from
t
h
e
list
s
in s
h
a
re/top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added residue and atom renaming
f
or AMBER
d
na and rna
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ad
d
ed D
N
A and RNA to the pdb2gmx
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
renamed O to O2 in amber r
n
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added natoms_
f
orce
_
constr t
o
t
_
for
c
erec
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 Hess
remov
e
d
g
a
rbage from
checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (rare) inc
o
rrect re
s
idue
numbe
r
s when
usi
n
g
g
mx_mt
o
p_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk
H
ess
ad
d
ed openm
m
wr
a
p
pe
r
R
F
paramet
e
r che
c
ks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hes
s
minor update to t
h
e pr
e
vios appendi
n
g
f
i
x
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
fixed m
d
ru
n
ap
p
end ch
e
ck when requested ou
t
put file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk Hes
s
added m
d
p
p
ara
m
e
ter for FE
d
H
t
a
b
les
commit
|
commitdiff
|
tree
2010-07-05
Ber
k
Hess
chang
e
d the defau
l
t
ma
x
imum
n
u
m
ber
of backup
s
from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk
H
ess
removed a lot of
slow
FFT gr
i
d si
z
es from calc_g
r
id
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
d
o
cument
e
d pull cosine we
i
ghting
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
renamed mdrun -cptnum to -
c
pnum
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
add
e
d
mdrun -cptnum optio
n
to keep
and
numbe
r
c
h
e
c
kpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
ess
rev
e
rted accide
n
tia
l
change of ta
b
a
ng
l
es in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
e
rk
H
es
s
added include update
.
h t
o
coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k
Hes
s
ad
d
e
d
b
a
ck const to gmx_so
r
t
c
ompare par
a
ms for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Be
r
k H
e
ss
removed obsolete
f
f
tgrid cod
e
a
n
d di
s
abled
P
PPM
with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hes
s
changed pdb2gmx
w
ater model atom co
u
n
t
detection
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk Hess
implem
e
nted nsteps=-1 for
mdr
u
n continuation
and tpbconv
commit
|
commitdiff
|
tree
2010-06-24
B
erk Hess
fi
x
ed smalloc
.
h and
small
o
c
.
c definition inconsis
t
encies
commit
|
commitdiff
|
tree
2010-06-24
Be
r
k
Hess
Merge bra
n
ch 'ma
s
t
er'
o
f git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-23
Be
r
k Hess
r
e
mo
v
ed s
t
atusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixe
d
g
m
x_enec
o
n
v com
p
iler warnings
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fixed eneconv -dt o
p
tion temp
o
rarily not w
r
i
ting averages
commit
|
commitdiff
|
tree
2010-06-22
Berk He
s
s
corrected edr
f
orma
t
issue introd
u
ced to
d
ay
commit
|
commitdiff
|
tree
2010-06-21
B
erk Hess
add gmx_qsort routine,
s
i
n
ce gli
b
c
qsort is
not thr
e
adsafe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixed typo
in fatal_error
call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now mdrun does not
writ
e
t
h
e tr
r
fil
e
wh
e
n
i
t
w
o
u
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Ber
k
Hess
a
dded env var GM
X
_MAXBACKUP
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fix for the previous mdrun
-re
r
un comm
i
t
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
m
drun -rer
u
n now reads the rerun traj only on the maste
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
mino
r
update fo
r
previous r
e
p
l
ex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Berk Hes
s
f
ixe
d
mdrun -rer
u
n g
i
v
ing NaN w
i
th dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
e
s
s
added water
m
odel sel
e
ction and li
s
t f
i
l
e
to pdb
2
gmx
commit
|
commitdiff
|
tree
2010-06-17
Berk H
e
ss
made
a s
e
parate ti
p
s3p
.
itp file
for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Merge bra
n
ch 'maste
r
'
of gi
t
@g
i
t
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
next