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fixed PME communication range when first DD dim is not x
2010-08-03
B
e
r
k Hes
s
fixed
P
ME
c
ommunicati
o
n rang
e
w
hen fi
r
st
DD dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Ber
k
Hess
mad
e
vr
e
sca
l
e and Berendsen tcouple wo
r
k with VV, altho
u
gh
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
B
erk Hess
correct
e
d LJ on
H of
c
harmm tip
s
3p
commit
|
commitdiff
|
tree
2010-07-29
B
e
rk H
e
ss
completed p
a
r
tial rename o
f
CY
N
to CY
S
for Amb
e
r
commit
|
commitdiff
|
tree
2010-07-28
B
erk Hess
cor
r
ected the Amber aminoacids
.
r2b
files
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
ess
r
enamed pme_
m
ax
s
hift0/1 to pme_maxshift_x/y
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
replaced the Charmm vsite parameters
(which were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hess
correc
t
ed a vsite paramete
r
in
the a
m
b
e
r ff's
commit
|
commitdiff
|
tree
2010-07-28
Be
r
k Hess
corrected Cl
atom n
a
m
e
in
amber
i
ons
.
itp
commit
|
commitdiff
|
tree
2010-07-28
Berk He
s
s
amber ff a
t
omtyp
e
s change: co
r
rected masses, removed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
updat
e
of amber03
ami
n
oacids
.
r
tp, accidentally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected mistakes i
n
amber03
g
b
s
a
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk
Hess
fixed typo in M
a
kefil
e
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
moved f
f
_
dum
.
it
p
to
t
he
g
mx a
n
d gromos ff
directories
commit
|
commitdiff
|
tree
2010-07-27
Ber
k
Hess
corrected the amb
e
r
vsite parameters
commit
|
commitdiff
|
tree
2010-07-27
Be
r
k
Hes
s
added h
i
s t
o
opls r2b file
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
made the ff file naming of amber and ch
a
r
m
m
co
n
sistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corre
c
ted th
e
amber water mod
e
l files
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PME deco
m
position check
for inverse DD order
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
r
enamed amber LYP to LYS a
n
d c
h
an
g
ed names for water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
removed HOH fro
m
amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
B
erk He
s
s
added missi
n
g entries for amb
e
r
r
na
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
cleaned up Amber hdb's and a
d
ded
HO4
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
ren
a
med atom type
s
from amber99_?
e
tc
.
t
o
the or
i
ginal
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
fi
x
ed
PME communication rang
e
(
no s
i
lent er
r
ors)
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk Hess
removed
buildin
g
block RT fr
o
m the lists in share/top
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added re
s
idue
a
nd ato
m
renaming
for AMBER dna and r
n
a
commit
|
commitdiff
|
tree
2010-07-26
B
er
k
Hess
added DNA and RN
A
to the pdb2gmx
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
named O to O
2
in
amber rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Ber
k
Hess
add
e
d natoms_force_constr to t_f
o
rc
e
r
e
c
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed O to O2 in amber dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Ber
k
H
ess
r
emo
v
ed garbage from check
p
oin
t
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk
H
ess
fixed (
r
are) incorrect residue numbers when usi
n
g gmx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk
H
ess
a
d
d
ed openmm
w
rapper
R
F
para
m
eter check
s
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
ess
min
o
r update to th
e
previo
s
a
ppending fix
commit
|
commitdiff
|
tree
2010-07-19
Be
r
k Hess
fix
e
d
m
dru
n
append
check wh
e
n
r
equ
e
ste
d
output
f
ile
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk
H
ess
add
e
d mdp p
a
rameter fo
r
FE dH table
s
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
c
h
anged t
h
e default max
i
mum num
b
er of backup
s
from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk
Hess
rem
o
v
ed a lot
of slow
FFT grid sizes from calc_grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
e
r
k Hess
documen
t
ed pull cosine
weighting
commit
|
commitdiff
|
tree
2010-06-28
B
erk Hess
r
e
named mdrun -cpt
n
u
m
to -cpnum
commit
|
commitdiff
|
tree
2010-06-28
Ber
k
Hes
s
added mdrun -cptn
u
m op
t
ion t
o
keep and
n
umber chec
k
points
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted accide
n
t
i
al change o
f
tabangles in gr
o
mpp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
added include update
.
h
to couplin
g
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
es
s
a
d
ded back const to g
m
x_sort compa
r
e par
a
m
s
for qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk
Hess
remo
v
ed ob
s
olete fftgr
i
d code an
d
dis
a
bled PPP
M
wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
changed pdb2gmx water mode
l
atom count detection
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
im
p
lement
e
d nsteps=
-
1 for mdrun c
o
ntinua
t
io
n
and tpbconv
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
fixed smalloc
.
h and smalloc
.
c defin
i
t
ion inconsistencies
commit
|
commitdiff
|
tree
2010-06-24
Berk
H
e
s
s
Merg
e
branc
h
'maste
r
' of git@git
.
gr
o
macs
.
o
r
g:
g
romacs
commit
|
commitdiff
|
tree
2010-06-23
Berk
Hess
removed statusi
o
.
h
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
f
ixed
g
mx_
e
neconv compi
l
e
r warn
i
ngs
commit
|
commitdiff
|
tree
2010-06-23
B
er
k
Hess
fixed eneconv -dt option temporar
i
ly not writi
n
g averages
commit
|
commitdiff
|
tree
2010-06-22
Ber
k
Hess
corr
e
cted e
d
r forma
t
issue introduc
e
d today
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
add gmx_qsort routine,
s
ince gl
i
bc qsort is n
o
t th
r
ea
d
safe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk
H
e
ss
fixed
t
y
po i
n
f
a
tal
_
error call
commit
|
commitdiff
|
tree
2010-06-18
B
e
r
k Hess
no
w
md
r
u
n
does not write t
h
e trr file when
it would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
added env
v
ar G
M
X_MAXBAC
K
UP
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
fix
for the previous mdrun -
r
erun comm
i
t
commit
|
commitdiff
|
tree
2010-06-17
Berk He
s
s
md
r
un -reru
n
now reads the rerun traj only
o
n the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
minor update for previou
s
r
eplex bugfix
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
f
ixed mdrun -rerun giving NaN w
i
th d
i
sp
c
o
rr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
added
wa
t
er model s
e
lection
a
nd
list file to pdb2gm
x
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
made a se
p
a
r
ate tips3
p
.
itp file for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
M
e
rge
branch
'master' of git@git
.
gromacs
.
org:
g
ro
m
acs
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
a
d
d
ed sp
c
e to charmm27
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixed
M
PI crash whe
n
nat_home=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
rest
o
red the old
order of
t
he mdrun option a
n
d remov
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
repla
c
ed more
gmx
_
fatal
by collecti
v
e cal
l
s
i
n DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fi
x
e
d
atom naming in encad c-term
i
ni
commit
|
commitdiff
|
tree
2010-06-16
B
e
rk
H
ess
wit
h
nste
p
s
=-1 m
d
run
now
prints ns/day estima
t
e
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
added nsteps=-1 option to mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
a
l
l
e
nergy minimizers now
d
o
0 steps wi
t
h nsteps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk
Hess
f
i
xed incor
r
ect pdb2gmx CYS2 to CYS renaming whic
h
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
B
e
rk Hess
allvsall loops n
o
w t
r
igger particle decomposition
commit
|
commitdiff
|
tree
2010-06-15
Berk He
s
s
fatal
_
error in the D
D
initializatio
n
now c
a
lls MPI
_
Fin
a
l
i
ze
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk Hess
added
-cw
d
option to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-11
Berk Hes
s
f
i
xed
mdr
u
n counter r
e
s
e
tting issues
commit
|
commitdiff
|
tree
2010-06-11
B
e
rk Hess
optimize
d
the number of thr
e
ad
s
commit
|
commitdiff
|
tree
2010-06-10
Berk
Hess
made DD wo
r
k
properly wi
t
h all
n
o
n-p
e
riodic sys
t
e
m
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Berk
H
ess
added more exp
l
anation
to i
d
ef
.
h
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
fixed uninitialized va
r
iable in do_md
commit
|
commitdiff
|
tree
2010-06-10
B
e
rk H
e
ss
fixed particle dec
o
m
p
osition loa
d
prin
t
commit
|
commitdiff
|
tree
2010-06-04
Berk Hess
fixed pdb2
g
mx me
s
s
i
ng up coord
i
nates when dele
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Ber
k
Hess
add
e
d notes on
m
dp disre
p
arame
t
e
r
s
commit
|
commitdiff
|
tree
2010-06-03
Berk
H
e
ss
distance restraint
e
nsembl
e
averaging is no longe
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
fixed bug i
n
enum parsing error me
s
sage
commit
|
commitdiff
|
tree
2010-06-03
Berk H
e
ss
added VV parameters to mdp_o
p
t
.
html
commit
|
commitdiff
|
tree
2010-06-02
Berk
H
es
s
fixed
m
ore Gromos atom type name cas
e
s
commit
|
commitdiff
|
tree
2010-06-01
Berk
Hess
cleaner fix for at
o
m type case is
s
ue with
G
B
para
m
ete
r
s
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixed atom type cas
e
issue
wi
t
h
G
B
paramete
r
s
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fixe
d
two
G
B bugs
commit
|
commitdiff
|
tree
2010-05-19
Be
r
k
H
ess
f
i
xed mdrun unwantingly modifyi
n
g nstenergy and n
s
tlog
commit
|
commitdiff
|
tree
2010-05-18
Berk Hess
implement SSE exp calcu
l
ation
f
or
s
olve_pme
commit
|
commitdiff
|
tree
2010-05-17
B
e
rk Hes
s
fixed some genbo
r
n include fil
e
details
commit
|
commitdiff
|
tree
2010-05-17
B
erk Hess
r
e
o
rder
e
d pme_solve_yzx
argu
m
ents
commit
|
commitdiff
|
tree
2010-05-14
Be
r
k
Hes
s
minor pme_solve v
i
ria
l
op
t
imization
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
fixed s
e
gv with mdrun -npm
e
1
commit
|
commitdiff
|
tree
2010-05-12
Berk He
s
s
fixe
d
case o
f
atom typ
e
s in th
e
G
romos force fields
commit
|
commitdiff
|
tree
2010-05-12
Berk Hess
corrected pdb2gmx force
fiel
d
comm
e
nts
commit
|
commitdiff
|
tree
next