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added some comment to group grompp assignment options
2010-08-18
Be
r
k Hess
added some comment to gr
o
up grompp
a
ssi
g
nment options
commit
|
commitdiff
|
tree
2010-08-18
Ber
k
Hess
ad
d
e
d
grou
p
c
omparis
o
n to gmxcheck and print groups
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Berk
Hess
fixed possible pathe string buffer ove
r
f
l
ow
in get
_
l
i
bdir
commit
|
commitdiff
|
tree
2010-08-17
Berk Hess
a
dded f
u
n
c
tio
n
rescal
e
_vel
o
citie
s
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx
_
r
m
p
bc now guesses ePB
C
again f
o
r
ea
c
h frame
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
gmx_rmpbc gets natoms pass
e
d agai
n
, without natoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
put omp
p
ragma's
i
n fft5d
.
c
b
e
twee
n
ifdef's
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k Hess
added
openmp prag
m
a's for the fft5d transpose routin
e
s
commit
|
commitdiff
|
tree
2010-08-16
Berk
Hess
fixe
d
mdr
u
n
writes tp
i
dist
.
x
v
g
o
n all nodes
commit
|
commitdiff
|
tree
2010-08-16
Be
r
k
H
ess
fixed se
g
v in m
d
r
un with
r
e
plica e
x
change
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
f
i
x
e
d fatal err
o
r in md
r
un
file appending with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
B
erk Hess
gmxche
c
k now prints rmsd's as %g is
o
%f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
m
oved f
u
ll precision real format d
e
f
i
n
i
tion to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Be
r
k He
s
s
reverted the last, non-co
s
metic
c
ha
n
ge to p
m
e
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk
Hes
s
m
i
nor
c
osmetic changes in
p
me
.
c
commit
|
commitdiff
|
tree
2010-08-12
Be
r
k Hes
s
made the
p
db
2
gmx oc
c
upancy warning m
o
re
obvious
commit
|
commitdiff
|
tree
2010-08-12
Berk Hes
s
fi
x
ed incorrect p
d
b2gmx output w
i
th
mult
i
ple (altlo
c
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
B
erk Hess
remove
d
-mer
g
e from t
h
e
pdb2g
m
x manual and clari
f
ied
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
B
erk H
e
ss
fixed bug th
a
t caused a segv when snew failed
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
r
e
move
d
CYS2 fro
m
the Am
b
er rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk Hes
s
removed pdb2gmx -cysh
h
i
dden option tha
t
s
hould hav
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk Hess
made mdru
n
-
sep
p
ot work with threads and -s
e
p
pot now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
Merge
b
r
a
n
ch 'release-4-5
-
patc
h
es' of
git@git
.
gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
c
o
rrected the (
i
rr
e
levant) defaul
t
ir
-
>gb_dielectri
c
_
o
ffset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
added -pbc option
t
o
g_traj
commit
|
commitdiff
|
tree
2010-08-05
B
erk Hess
readinp,
used for e
.
g
.
mdp, no longer
uses gm
x
c
p
p
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
fixed
gm
x
_
rm
p
bc undoing
the
shifting when x!=x_s
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
sc_sigma
no
w
also sets the minimum
v
alue
f
or the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
B
e
rk Hess
m
ake_ndx no
w
all
o
ws ne
a
rly all character
s
i
n a
t
om and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk H
e
s
s
g
mxcheck now
comp
a
re
s
terms by name ma
t
ching
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
r
emo
v
ed
commrec->nthrea
d
s from FAHCORE code
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
gmxcheck now
usi
n
g the diagonal for relative tolerance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
er
k
H
ess
fixed g_
e
nergy manual form
a
tting i
s
sues
commit
|
commitdiff
|
tree
2010-08-04
Berk He
s
s
grompp automatic nstcalcen
e
rgy
setting now takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk
H
e
ss
a
dded full
p
r
e
cision option to g_
t
raj and reformatted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
fixed PME communicat
i
on ran
g
e wh
e
n first
D
D dim i
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
made vrescal
e
an
d
Berendsen
t
couple wo
r
k with VV, alth
o
ugh
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
corrected L
J
o
n H o
f
charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
B
erk H
e
ss
completed
partial rename of CYN to C
Y
S for
A
m
b
er
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
es
s
co
r
rected the Amber ami
n
oacids
.
r2b
files
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k Hess
renamed pme_max
s
hift0/1 to
p
m
e
_maxsh
i
ft_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
replaced the
C
harmm vs
i
te parameters
(whi
c
h were
OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
correcte
d
a
vs
i
t
e
para
m
eter in the
amber ff
'
s
commit
|
commitdiff
|
tree
2010-07-28
B
e
r
k He
s
s
c
or
r
ected Cl
atom name in amber ions
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber
f
f ato
m
types change:
c
orre
c
ted masse
s
, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
upd
a
t
e
of
amber03 aminoacids
.
r
tp, a
c
ciden
t
a
l
l
y
le
f
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
B
e
r
k
Hes
s
corr
e
cted mis
t
a
k
es in amber03 gbsa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
e
ss
f
i
xe
d
typo in M
a
k
e
f
i
le
commit
|
commitdiff
|
tree
2010-07-27
Berk
Hess
m
o
v
e
d ff_dum
.
it
p
to the gmx and gromos ff di
r
ec
t
ories
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected th
e
amber vsite parameters
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
added his to opls r2b fi
l
e
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made the ff
file naming o
f
amber and
c
harmm
co
n
sistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
B
erk H
e
ss
corrected th
e
a
mber
w
a
ter model f
i
les
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fi
x
e
d PME decomp
o
sition
c
heck
fo
r
inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ren
a
med amber LYP to LYS and changed names for w
a
ter
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
removed
H
OH from
a
mber rna
.
h
d
b
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
a
dded missing entries
f
or amb
e
r
rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
cle
a
ne
d
up Amber hdb's and a
d
ded HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
nam
e
d a
t
om types from
a
mb
e
r9
9
_? etc
.
t
o
the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hes
s
fixed PME
c
ommunication range (no silent errors)
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
removed build
i
ng bl
o
c
k RT from t
h
e lists in share/top
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
ad
d
ed
r
esidu
e
an
d
atom
r
enaming for
A
M
B
ER dna and
r
na
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
a
dded DNA and RNA
t
o
t
he pdb2gmx
.
ar
n
fo
r
m
a
t
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
re
n
amed O to
O2
i
n
amber
rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
added
natom
s
_f
o
rce_co
n
s
t
r to t_forcerec
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
rename
d
O
t
o O2 in amber
dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
B
e
r
k
H
e
s
s
removed garbage from checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (rare) in
c
orrect residue num
b
ers when usi
n
g gm
x
_
mt
o
p_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
added
o
penmm
w
ra
p
per RF parameter checks
commit
|
commitdiff
|
tree
2010-07-19
Be
r
k Hess
minor update to the
previ
o
s appe
n
ding
f
i
x
commit
|
commitdiff
|
tree
2010-07-19
Berk H
e
ss
fixed mdrun append check when reque
s
t
ed output file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
B
e
rk Hess
add
e
d
mdp parameter
f
o
r
FE dH table
s
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
changed the
d
e
faul
t
maximum number of backu
p
s
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
rem
o
ved a lot of slow FFT
g
r
id siz
e
s
f
rom calc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
erk Hess
d
o
cumen
t
ed pul
l
c
o
s
ine weighting
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k
Hess
rename
d
mdrun -cptnum to -cpnum
commit
|
commitdiff
|
tree
2010-06-28
B
e
rk Hess
added md
r
un
-
cptnum opt
i
on to ke
e
p
a
nd num
b
er
checkpoin
t
s
commit
|
commitdiff
|
tree
2010-06-28
Berk H
e
ss
reverted accidential change of
t
abangles in
g
rompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
erk
H
e
ss
added include update
.
h
t
o coup
l
i
n
g
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk He
s
s
a
dded bac
k
co
n
st to
g
m
x
_sort compare params for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
r
emoved
o
b
solete
f
ftgrid co
d
e a
n
d disabled PPPM with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Be
r
k
H
ess
c
h
a
nged pdb
2
gmx water model
ato
m
count
detectio
n
commit
|
commitdiff
|
tree
2010-06-24
Berk Hes
s
implemented n
s
t
ep
s
=-1 for mdrun continuation an
d
tp
b
conv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fix
e
d smalloc
.
h a
n
d
smalloc
.
c definiti
o
n in
c
onsiste
n
cie
s
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge br
a
nch '
m
a
s
ter' of
g
it@git
.
gromac
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-06-23
Berk
Hess
removed st
a
tusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hes
s
fixed g
m
x_eneconv compiler warnings
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
fix
e
d
eneconv -dt
o
pti
o
n
t
e
m
pora
r
i
l
y
not
writing
average
s
commit
|
commitdiff
|
tree
2010-06-22
Be
r
k
H
e
ss
c
o
r
rected
edr format issue int
r
oduced today
commit
|
commitdiff
|
tree
2010-06-21
Berk
H
e
ss
add gmx
_
q
s
ort routine, sinc
e
glibc qs
o
rt
is n
o
t threa
d
safe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixe
d
typo in fatal_error
call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now mdr
u
n does
n
ot w
r
ite the tr
r
file
w
hen it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
added env v
a
r G
M
X_MAXBA
C
KUP
commit
|
commitdiff
|
tree
2010-06-17
B
erk Hess
fix for the
previous mdrun -rerun commit
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
mdrun
-
r
erun n
o
w
r
eads th
e
rerun tra
j
o
nly
o
n the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
B
erk
H
ess
minor upda
t
e for previo
u
s re
p
lex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fixed mdru
n
-r
e
ru
n
giving NaN
w
i
t
h dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
added
wa
t
e
r mod
e
l selection a
n
d list file to pdb
2
gmx
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
made
a
sep
a
r
ate tips3p
.
itp
file for
C
HARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Mer
g
e
branch
'
mas
t
e
r
' of git@g
i
t
.
grom
a
cs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
next