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gmxcheck now prints rmsd's as %g iso %f
2010-08-13
Berk Hess
g
m
xcheck now print
s
rms
d
'
s
as
%g iso %f
commit
|
commitdiff
|
tree
2010-08-13
Ber
k
Hess
moved full pr
e
c
i
si
o
n r
e
al
format defi
n
i
tion to si
m
ple
.
h
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
H
e
ss
reverted
the
l
ast, non-cosmetic c
h
ange to
pme
.
c
commit
|
commitdiff
|
tree
2010-08-12
Ber
k
Hess
minor cosmetic changes in p
m
e
.
c
commit
|
commitdiff
|
tree
2010-08-12
Berk Hess
m
a
de t
h
e
pdb2gmx occupancy warning mo
r
e
o
bv
i
ous
commit
|
commitdiff
|
tree
2010-08-12
Berk
H
e
ss
f
i
xe
d
in
c
orre
c
t
pdb2gmx outp
u
t with multiple (altloc
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Be
r
k Hess
removed -m
e
rge from the pd
b
2gmx
manual and
c
larif
i
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Berk Hess
f
ixed bug
t
h
at caused a segv when snew failed
commit
|
commitdiff
|
tree
2010-08-10
B
erk
Hess
remov
e
d CYS2 fr
o
m
t
he Am
b
er rtp files
commit
|
commitdiff
|
tree
2010-08-10
Berk He
s
s
rem
o
ved pdb2gmx -cysh hidden opt
i
on that
shoul
d
ha
v
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-09
Be
r
k He
s
s
made mdrun -se
p
po
t
wo
r
k with threa
d
s
a
nd -seppo
t
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Be
r
k H
e
ss
Merge branch
'release-4-5
-
patches' of git@
g
i
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
B
erk
H
ess
co
r
rected t
h
e
(irreleva
n
t
)
def
a
u
l
t ir->gb_di
e
l
ectric_
o
f
fset
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk
Hess
added -
p
bc option to g_traj
commit
|
commitdiff
|
tree
2010-08-05
Ber
k
Hess
r
e
ad
i
np, used for
e
.
g
.
m
d
p
,
no longe
r
us
e
s gmxcpp
commit
|
commitdiff
|
tree
2010-08-05
Berk
H
es
s
fixed gmx_rmpbc undoing
t
h
e
sh
i
f
ting when
x!
=
x_s
commit
|
commitdiff
|
tree
2010-08-05
B
e
r
k Hes
s
sc_sigma now also sets
t
he minim
u
m value
for the soft
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hes
s
m
a
ke_nd
x
now allows
nea
r
ly
a
ll chara
c
ters in a
t
om and
.
.
.
commit
|
commitdiff
|
tree
2010-08-05
Berk Hess
gm
x
c
heck now c
o
m
pares t
e
rms by name
m
atching
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
removed comm
r
ec
-
>nthreads fro
m
FAHCORE code
commit
|
commitdiff
|
tree
2010-08-04
B
e
rk Hess
gmxc
h
eck now us
i
ng the diagonal fo
r
relativ
e
toleranc
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
fixed g
_
ener
g
y
m
a
nual formatting issues
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
grompp auto
m
atic nstcalcenergy setting
now takes small
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Berk Hess
a
dd
e
d full p
r
ecis
i
o
n option to g_traj and r
e
f
orma
t
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk He
s
s
f
ixed
PME communica
t
ion ran
g
e when first D
D
dim
is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Berk Hes
s
m
a
d
e vr
e
s
c
ale and Berend
s
en
t
c
ouple work with VV, although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk H
e
ss
cor
r
ected LJ
on H
of charmm tips3p
commit
|
commitdiff
|
tree
2010-07-29
B
e
r
k Hess
completed partial renam
e
o
f
CYN
t
o CYS for Amber
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
corrected the Amber am
i
noa
c
ids
.
r2b
f
iles
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
ess
rename
d
p
m
e_m
a
x
shift0/1 to p
m
e_maxshift_x/
y
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
r
eplaced the Charmm vsite para
m
e
t
ers (whi
c
h w
e
re OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
e
r
k
H
ess
corr
e
cted
a vsite parameter in the amber ff's
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
correc
t
ed Cl atom na
m
e
in amber
i
ons
.
it
p
commit
|
commitdiff
|
tree
2010-07-28
Berk H
e
ss
amber ff ato
m
t
y
p
es cha
n
ge: corrected masses, re
m
oved
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
B
erk Hess
u
p
d
ate of amber03 ami
n
oacids
.
rtp, accidenta
l
ly left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
c
o
rrected mist
a
kes in amber03 gbsa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk Hes
s
fixed typo in Mak
e
file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
m
oved ff_dum
.
i
tp to the gmx and gromos ff directories
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
H
ess
cor
r
ected the amber
v
sit
e
parameters
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
added his to opls r2b
file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made
t
he f
f
file namin
g
of amber and charmm consist
e
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
corrected
t
h
e amber water mo
d
el files
commit
|
commitdiff
|
tree
2010-07-27
Berk H
e
s
s
fix
e
d PME dec
o
mposi
t
ion check for in
v
erse DD
order
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
renamed amber
LYP
to LYS and cha
n
ged
n
ames for w
a
t
er
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
removed HOH fro
m
amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ad
d
ed missing e
n
trie
s
for amber
rna
.
hd
b
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
cleaned up A
m
ber
hdb'
s
and added H
O
4
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
renamed atom
t
y
p
es f
r
om
a
mber99
_
?
etc
.
to the original
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
fixed P
M
E communica
t
io
n
ra
n
ge (n
o
sile
n
t errors)
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk He
s
s
removed building b
l
ock RT from the lists
in share/top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added
r
esidue and atom rena
m
i
n
g
f
or AMBER dna and rna
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added D
N
A and RNA to the pdb2gmx
.
ar
n
f
o
rmat
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
renamed
O to O2 in amber rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ad
d
ed na
t
oms_fo
r
ce_constr to t_forcerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
ren
a
med
O to
O
2
in am
b
er dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
B
e
rk Hess
removed garbage
f
rom
c
heckpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fixed (rare) inco
r
r
ec
t
residue numbers when
u
si
n
g gmx_mtop
_
a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
added ope
n
m
m wrapper R
F
paramet
e
r
c
h
ecks
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
e
s
s
min
o
r up
d
ate
to
t
he
previos appe
n
ding fix
commit
|
commitdiff
|
tree
2010-07-19
B
e
r
k Hess
f
i
xed
m
drun ap
p
en
d
c
h
eck when requested
o
ut
p
ut f
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
B
e
rk Hess
added mdp pa
r
ameter for
F
E dH table
s
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
c
h
ange
d
the default maximum numb
e
r
of backups f
r
o
m
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Ber
k
H
e
ss
removed a lot of slow FFT
gr
i
d sizes from c
a
lc_gri
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
d
o
c
umented p
u
l
l
cosine weighting
commit
|
commitdiff
|
tree
2010-06-28
Berk
Hess
rena
m
ed
mdrun -cp
t
n
u
m to -
c
pnu
m
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added mdrun -cptn
u
m
option to
k
e
ep and number chec
k
points
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted accidential change
o
f tabangles
in grom
p
p
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
a
dded include update
.
h to coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added back co
n
st to gmx_sor
t
compar
e
params for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
removed o
b
solete fftgrid code
a
nd dis
a
b
l
e
d PPP
M
w
i
th
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
c
h
ange
d
p
d
b
2
gmx wa
t
er model atom count detectio
n
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
implemented
nsteps
=
-1 f
o
r
mdrun continuation
a
n
d tpb
c
onv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fixed smalloc
.
h and small
o
c
.
c definition
inconsistencie
s
commit
|
commitdiff
|
tree
2010-06-24
Berk Hes
s
Merge br
a
nch '
m
a
s
ter' of git@git
.
g
ro
m
a
cs
.
or
g
:
gromacs
commit
|
commitdiff
|
tree
2010-06-23
Berk
H
ess
rem
o
ved
s
t
a
tusio
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
f
i
xed
g
mx_eneconv compiler warnings
commit
|
commitdiff
|
tree
2010-06-23
B
erk
H
ess
fixed
eneconv -dt option temporarily not writing
a
verag
e
s
commit
|
commitdiff
|
tree
2010-06-22
Berk
Hess
corrected ed
r
format
issue i
n
trod
u
ced today
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
ad
d
gmx_
q
s
or
t
routine, since
g
lib
c
qsort is not th
r
eads
a
fe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixed typo in fata
l
_e
r
r
o
r call
commit
|
commitdiff
|
tree
2010-06-18
Ber
k
H
e
ss
now mdrun do
e
s not write the
trr file when it wou
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
added env
var G
M
X
_
MAXBACK
U
P
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
fix for th
e
pre
v
ious
mdr
u
n -r
e
run com
m
it
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk He
s
s
mdru
n
-reru
n
now read
s
t
h
e rerun traj only on
the m
a
ster
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
minor update for previous replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fixe
d
md
r
u
n -re
r
u
n g
i
ving
N
a
N
w
i
t
h dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
added w
a
ter
model selection and list file to
pdb
2
gmx
commit
|
commitdiff
|
tree
2010-06-17
Ber
k
H
ess
m
ade a sep
a
ra
t
e
tips3
p
.
i
t
p file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Mer
g
e b
r
anch
'
m
a
s
ter
'
o
f
git@git
.
groma
c
s
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
ess
ad
d
e
d s
p
ce to charm
m
2
7
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixed MPI crash when nat_home=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
restored
t
he
o
ld order of the
mdrun option and rem
o
v
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hes
s
replaced more g
m
x_fat
a
l by collective c
a
l
l
s
i
n
D
D
commit
|
commitdiff
|
tree
2010-06-16
Be
r
k Hess
fixed atom n
a
ming in encad c-
t
ermini
commit
|
commitdiff
|
tree
2010-06-16
Ber
k
Hess
with nsteps=-1 mdrun now prints ns/day est
i
ma
t
e
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
added nsteps=-1 option to
mdp_opt
.
h
t
ml
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
all e
n
ergy min
i
miz
e
rs
now do 0 steps with nsteps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fix
e
d
in
c
orre
c
t pdb2gmx
C
YS2 to CY
S
renaming
w
hich
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
allvsa
l
l
l
o
o
ps now trigger particle
decom
p
o
s
ition
commit
|
commitdiff
|
tree
2010-06-15
Berk
Hess
f
a
tal_error
i
n
the
D
D
initiali
z
ation now ca
l
l
s
M
P
I_Finalize
.
.
.
commit
|
commitdiff
|
tree
next