repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
gmx_rmpbc gets natoms passed again, without natoms many tool could not parse trajecto...
2010-08-16
Berk Hess
g
mx_rmpbc
g
ets
n
atoms passed again, without n
a
toms
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Berk H
e
ss
put omp pragma's in f
f
t
5
d
.
c be
t
ween
ifd
e
f's
commit
|
commitdiff
|
tree
2010-08-16
Berk Hess
adde
d
o
penmp pragma's
for t
h
e fft5d tran
s
pose routines
commit
|
commitdiff
|
tree
2010-08-16
Berk
He
s
s
fixe
d
m
d
run writes tpidist
.
xvg on all nodes
commit
|
commitdiff
|
tree
2010-08-16
Berk
H
ess
fi
x
ed segv
i
n
mdrun
with replica exchange
commit
|
commitdiff
|
tree
2010-08-16
B
e
rk Hess
f
ixed
f
a
t
a
l e
r
ror
i
n
mdrun
f
il
e
appending with -multi
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
B
e
rk
H
ess
gmxcheck now prin
t
s rm
s
d's as %g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Berk Hess
move
d
f
ull precision real format
d
efiniti
o
n to simple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
reverted the
last, non
-
cosmetic c
h
an
g
e to pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
minor cosmetic changes in pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
B
er
k
Hess
made
t
h
e
p
d
b2gmx occupancy warning more o
b
v
i
o
us
commit
|
commitdiff
|
tree
2010-08-12
B
e
rk He
s
s
fixed inco
r
rect pdb2gmx ou
t
put wit
h
multiple (altloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
re
m
oved -merge
f
rom
t
he pdb2gmx manual and clarified
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
fixed
b
ug that ca
u
se
d
a segv wh
e
n
snew failed
commit
|
commitdiff
|
tree
2010-08-10
Berk
Hess
remo
v
ed CYS2 fro
m
the Amber rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk Hess
remov
e
d pdb2gmx -c
y
sh hi
d
den option tha
t
should have
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Berk Hess
m
a
de mdrun -seppot work
w
ith threads an
d
-seppot now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
Merge branch 'release-
4
-5-patches' of gi
t
@git
.
gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Berk Hess
corrected the (
i
rrelevant) defa
u
lt
i
r
->gb_di
e
lec
t
ri
c
_offset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
H
ess
added -pbc op
t
ion
t
o g_tra
j
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
re
a
dinp, used f
o
r e
.
g
.
mdp, no longe
r
u
ses gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
e
ss
fixed gmx_rmpbc undoing the s
h
ifting when x!=
x
_s
commit
|
commitdiff
|
tree
2010-08-05
Berk He
s
s
sc_sigma now al
s
o sets th
e
mini
m
um va
l
ue for the
s
oft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Be
r
k H
e
ss
make_nd
x
no
w
allows nearly all
character
s
i
n
atom and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
ess
gmxcheck now compares ter
m
s by name matc
h
ing
commit
|
commitdiff
|
tree
2010-08-04
Berk H
e
ss
removed c
o
mmrec-
>
nthreads from
FAHCORE code
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
gmxcheck now us
i
ng the di
a
g
o
nal
f
or relative
tolerance
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
f
ix
e
d g_ene
r
gy manu
a
l
formatting
i
ssues
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hes
s
gr
o
mpp automatic
nstcalcene
r
g
y
s
et
t
ing no
w
takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hes
s
ad
d
ed full precisio
n
option to g_traj and reform
a
tted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hes
s
f
i
x
ed PME c
o
mmuni
c
a
tio
n
range
w
h
en f
i
rst DD dim
i
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hess
made vrescale and Berendsen tcouple work
with VV, a
l
t
ho
u
gh
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk
H
ess
corrected LJ on H of ch
a
rmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
B
erk Hess
com
p
l
e
ted
p
artial rename of CYN to CYS
fo
r
Amb
e
r
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected the Amber aminoacids
.
r2b files
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
re
n
a
m
e
d pme_max
s
hift0/1 to pm
e
_maxshift_x/
y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
re
p
lac
e
d the Charmm vsite
pa
r
a
meters (which
w
ere OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk H
e
ss
corr
e
c
t
ed
a
vsi
t
e parameter in the amber f
f
's
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k Hess
corrected
Cl atom name in amber ions
.
i
t
p
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
amber
ff atomtypes
ch
a
n
g
e: correc
t
ed mas
s
es, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
updat
e
o
f
a
mber03
a
m
inoacids
.
rtp, accidenta
l
ly left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hes
s
corrected
mi
s
takes in amber
0
3 gbsa
.
i
tp
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed
typo
in Makefil
e
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk Hess
m
oved ff_dum
.
i
t
p to the gmx and
gromos ff dire
c
tories
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k Hess
correc
t
e
d
t
h
e amber vsite
parameters
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
ss
added
his
t
o
opls
r
2
b
file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made
the ff
f
ile naming
of amber and charmm cons
i
stent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
ss
co
r
rected
t
he amber water mo
d
e
l files
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PM
E
decom
p
ositi
o
n che
c
k for inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
rename
d
amber LYP to
L
YS a
n
d changed names for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
removed
HOH
from amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added missin
g
entrie
s
for amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
cleaned up Amber hdb
'
s
and a
d
ded HO4
commit
|
commitdiff
|
tree
2010-07-26
Berk
Hess
rena
m
ed atom
ty
p
es from amber99_? e
t
c
.
to
t
he original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fix
e
d PME commu
n
i
cation range (no silent errors)
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
remov
e
d
building
b
loc
k
RT fro
m
the lists
i
n share/top
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
added residue and atom
renaming for AMBER dna and
rna
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
a
d
ded DN
A
and RNA to
t
h
e
pdb2
g
m
x
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Berk H
e
ss
renamed O to O
2
in amber r
n
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
add
e
d nat
o
ms_force_c
o
nstr to t_f
o
rcerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
en
a
med O to O2 in amber d
n
a
.
r
tp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
re
m
o
v
ed
garba
g
e
fr
o
m checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (rare) incorrect res
i
d
ue numb
e
rs when
using g
m
x_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Be
r
k Hess
added ope
n
mm
w
r
a
p
per RF param
e
ter
c
hecks
commit
|
commitdiff
|
tree
2010-07-19
B
e
r
k Hess
minor update to the previ
o
s appen
d
ing
fi
x
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
fixed md
r
un append check
when
r
equeste
d
output
fil
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
B
erk Hess
added mdp parameter f
o
r FE
d
H
t
able
s
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
changed the
d
efault ma
x
im
u
m
num
b
e
r
of backups
from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Ber
k
Hess
removed a lot of slo
w
FFT g
r
id sizes from calc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
documented pull co
s
in
e
wei
g
hting
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
e
s
s
r
enam
e
d mdrun -cptnu
m
to -cpnu
m
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
add
e
d mdru
n
-cptnum optio
n
to k
e
ep and
n
umber checkpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
r
e
ver
t
ed accide
n
tial chan
g
e o
f
tabangles in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added include update
.
h to
c
oupl
i
ng
.
c
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k Hes
s
adde
d
back co
n
s
t to gmx_sort compare params for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk He
s
s
removed ob
s
olete fftgrid
code and disa
b
led PPPM with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
B
erk He
s
s
c
h
anged
pdb2g
m
x water model atom count d
e
tecti
o
n
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
implemented nsteps=-1 for mdru
n
continuation and tpbconv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fixed smalloc
.
h and sma
l
loc
.
c
d
efinition i
n
consistencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
Merge branch 'master'
o
f git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-23
B
e
rk Hess
remo
v
e
d
statusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Ber
k
H
e
s
s
fixe
d
gmx_
e
neconv compiler w
a
rnings
commit
|
commitdiff
|
tree
2010-06-23
B
erk
H
ess
f
ixed eneconv -dt
o
pti
o
n te
m
porarily no
t
writing
averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
corrected edr for
m
at issu
e
introduced
today
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
add gm
x
_qsort routine, since g
l
ibc qsort
is no
t
t
h
readsafe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
B
er
k
Hess
fixed typo in fat
a
l_error call
commit
|
commitdiff
|
tree
2010-06-18
Berk
H
ess
no
w
mdrun does not write the trr file
when it
w
ould
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk H
e
ss
added env
v
ar GMX
_
MAXBAC
K
UP
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
fix for
t
he
previous
m
d
run -rerun c
o
mmit
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k Hess
mdrun
-
re
r
un now reads the rerun traj only
o
n the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
Hess
minor update
f
o
r
previous replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
fixed mdrun -re
r
un giving Na
N
w
i
th disp
c
o
rr
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
H
e
s
s
added water mo
d
el
selec
t
ion and list file
t
o pdb2gm
x
commit
|
commitdiff
|
tree
2010-06-17
B
erk Hess
made
a
separa
t
e tips3p
.
itp fil
e
for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Merge branch 'master' of git@git
.
g
romacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-06-16
Be
r
k
H
e
s
s
added spce to charmm27
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fi
x
ed MPI crash
w
hen nat_hom
e
=0
i
n D
D
commit
|
commitdiff
|
tree
2010-06-16
Berk H
e
ss
restored the old order of the
mdrun option and re
m
oved
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
B
erk Hess
r
eplaced more gm
x
_fatal by collective
c
a
l
l
s
in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
f
i
xed ato
m
naming i
n
encad c
-
termini
commit
|
commitdiff
|
tree
next