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fixed PME communication range when first DD dim is not x
2010-08-03
Berk Hess
fixed PME
c
o
m
mu
n
ication range
w
hen first DD
dim is
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
Be
r
k
H
e
ss
made vrescale and Berendsen tcou
p
l
e
work with
V
V, although
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Berk Hess
cor
r
e
cted LJ on H o
f
charmm tip
s
3p
commit
|
commitdiff
|
tree
2010-07-29
B
erk
Hess
compl
e
t
e
d parti
a
l rename of
C
YN to CYS
f
or
A
m
b
er
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
Hess
cor
r
ected the Amber aminoacids
.
r2b
files
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
H
e
ss
r
e
named
p
me_maxshift0/1 to
pme_maxshift_x/y
commit
|
commitdiff
|
tree
2010-07-28
Ber
k
Hess
r
e
plac
e
d the Char
m
m vsi
t
e p
a
ram
e
t
e
r
s
(
w
hich were OPLS
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk Hes
s
corrected a vsite para
m
et
e
r in the a
m
ber ff's
commit
|
commitdiff
|
tree
2010-07-28
B
e
rk Hes
s
cor
r
ected
C
l atom name in amber ions
.
i
t
p
commit
|
commitdiff
|
tree
2010-07-28
Berk
Hess
a
mber ff atomtype
s
change
:
cor
r
ec
t
ed mas
s
es,
r
em
o
v
ed
.
.
.
commit
|
commitdiff
|
tree
2010-07-28
Berk
H
ess
u
p
date of amber03 aminoacids
.
rtp, acciden
t
ally left
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk He
s
s
correcte
d
mistakes in a
m
b
e
r03 g
b
sa
.
itp
commit
|
commitdiff
|
tree
2010-07-27
Berk He
s
s
f
i
xed typo
i
n Makefile
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
mov
e
d
ff
_
dum
.
itp
t
o the g
m
x and gro
m
os ff directories
commit
|
commitdiff
|
tree
2010-07-27
Berk
H
ess
corr
e
cted the a
m
b
er vsite paramete
r
s
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
added h
i
s to opls r
2
b file
commit
|
commitdiff
|
tree
2010-07-27
B
e
rk Hess
made the ff file
naming
of
amber a
n
d charmm consistent
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
corrected
t
h
e amber water m
o
d
el files
commit
|
commitdiff
|
tree
2010-07-27
Berk Hess
fixed PME decomposition check for inverse D
D
o
r
der
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
rename
d
amber LYP to LY
S
and changed names for wat
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hes
s
removed HOH
from amber rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
add
e
d miss
i
ng e
n
tries for amber rna
.
h
d
b
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
cle
a
n
e
d
up Amber hdb's and added
HO4
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hes
s
renamed atom types
f
rom
a
m
b
e
r99_?
e
tc
.
to
t
he o
r
igi
n
al
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fixed P
M
E
communication range
(
no sil
e
nt
e
rrors)
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
r
e
moved b
u
il
d
ing bl
o
ck RT
f
rom the li
s
ts in shar
e
/
t
op
commit
|
commitdiff
|
tree
2010-07-26
Berk H
e
s
s
added r
e
sidue and atom r
e
naming
f
or AMBE
R
dna and rn
a
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
a
dded
D
NA and RNA to
the pdb2gm
x
.
arn for
m
at
commit
|
commitdiff
|
tree
2010-07-26
Berk He
s
s
renamed O to O2 in amber rn
a
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added n
a
toms_force_con
s
t
r
to t_f
o
r
c
e
rec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
renamed O to O2 in amb
e
r
dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk Hes
s
removed
g
arbage from checkpoin
t
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
fi
x
ed (rar
e
) incorrect
residue num
b
e
rs
w
hen using gmx_mto
p
_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Be
r
k Hess
a
d
ded ope
n
m
m wrapp
e
r RF
p
a
rameter ch
e
c
ks
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
mino
r
update to the previos
append
i
ng fix
commit
|
commitdiff
|
tree
2010-07-19
Berk
H
e
ss
fixed mdrun
a
ppend check when requested
outpu
t
f
i
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
B
erk Hess
added
m
dp par
a
meter for FE dH tables
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
c
hanged th
e
d
e
f
ault m
a
x
i
m
u
m number
o
f backups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk He
s
s
removed a lot of
slow FFT gr
i
d si
z
es
from cal
c
_
gri
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
erk Hess
documented pull cosine weighting
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
rena
m
ed
md
r
un -
c
ptnum to -cpnum
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
added mdrun
-cptnum o
p
tio
n
t
o
keep and
number checkpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted accid
e
ntial chang
e
of tabangle
s
in grompp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
erk Hess
adde
d
include update
.
h t
o
coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Be
r
k H
e
ss
adde
d
back
co
n
s
t
to gmx_sort compare params f
o
r
qsort
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
B
erk
H
es
s
removed ob
s
o
lete
f
f
t
grid
c
ode and disabled
P
PP
M
w
ith
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk H
e
ss
c
hanged pdb
2
gmx water mode
l
a
t
o
m coun
t
detection
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
i
mpl
e
me
n
t
e
d nsteps=-1 for md
r
un continuation and tpbconv
commit
|
commitdiff
|
tree
2010-06-24
Berk
H
e
ss
fixe
d
smalloc
.
h and smal
l
oc
.
c definition i
n
consisten
c
ies
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk Hess
Merge b
r
a
n
ch 'maste
r
'
o
f git@git
.
gr
o
m
acs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-23
B
e
rk Hess
removed
s
tat
u
sio
.
h
commit
|
commitdiff
|
tree
2010-06-23
B
erk He
s
s
fixed gmx_eneconv co
m
p
i
ler wa
r
nings
commit
|
commitdiff
|
tree
2010-06-23
Berk Hes
s
f
ixe
d
e
n
e
c
onv -dt option te
m
p
orarily
not wri
t
ing avera
g
e
s
commit
|
commitdiff
|
tree
2010-06-22
Berk
H
ess
corrected edr format issue
i
ntroduced today
commit
|
commitdiff
|
tree
2010-06-21
B
erk He
s
s
add gm
x
_q
s
ort routine, since
glibc qso
r
t
is not
thread
s
af
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fixed typ
o
in fatal_error call
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
now mdrun do
e
s
not write the trr
fi
l
e when
i
t would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
add
e
d env var
G
MX_MA
X
BACKUP
commit
|
commitdiff
|
tree
2010-06-17
B
e
r
k H
e
ss
fix for the prev
i
o
us
m
d
r
un
-rerun c
o
mmit
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
mdrun
-
r
erun now
r
eads the rer
u
n tra
j
only on the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
ess
m
i
no
r
u
pda
t
e for
p
rev
i
o
us r
e
p
le
x
bugf
i
x
commit
|
commitdiff
|
tree
2010-06-17
Berk
H
e
ss
fixed mdru
n
-rer
u
n gi
v
in
g
NaN wi
t
h
dispc
o
r
r
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk Hess
added water
m
odel s
e
lection
a
nd lis
t
file to pdb2gmx
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
made a
s
eparate
t
ips3p
.
itp file f
o
r CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Merge branch 'm
a
ster' of git@git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
a
d
d
e
d
s
p
ce
to c
h
armm27
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
f
ixed
MPI crash when nat
_
h
ome
=
0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
res
t
ored the old order
of the mdrun option and removed
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
replaced more gmx
_
fatal by collect
i
ve
calls in
D
D
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
fixed a
t
o
m
naming
in encad c-termini
commit
|
commitdiff
|
tree
2010-06-16
Berk H
e
ss
with
nsteps=-1
mdrun now prints
ns/day e
s
timate
commit
|
commitdiff
|
tree
2010-06-16
B
e
r
k
He
s
s
added nste
p
s
=
-1 option
t
o mdp
_
o
pt
.
ht
m
l
commit
|
commitdiff
|
tree
2010-06-16
B
e
rk Hess
a
l
l energy mini
m
izers now do 0 steps with nst
e
ps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hess
fixed incorrect pdb2gmx CYS2 to C
Y
S renaming which
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Ber
k
Hess
allvsall lo
o
ps now tr
i
gger
particle deco
m
positio
n
commit
|
commitdiff
|
tree
2010-06-15
Be
r
k Hess
f
a
tal_error in
the DD initialization now c
a
lls MPI_Finaliz
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Berk Hess
ad
d
ed -cwd option to
p
db2gm
x
commit
|
commitdiff
|
tree
2010-06-11
B
e
rk Hess
fixed mdrun counte
r
resetting issues
commit
|
commitdiff
|
tree
2010-06-11
Berk Hess
optimize
d
the number of threads
commit
|
commitdiff
|
tree
2010-06-10
Berk
H
e
ss
made DD work p
r
operly
with
a
l
l
n
on-peri
o
dic sys
t
em
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
adde
d
mor
e
e
x
planation to idef
.
h
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
fixed uninitialized variabl
e
in do_md
commit
|
commitdiff
|
tree
2010-06-10
Ber
k
H
ess
fixed particle d
e
composition load
prin
t
commit
|
commitdiff
|
tree
2010-06-04
B
erk Hess
fi
x
e
d pdb2
g
mx me
s
sing up coordina
t
es when dele
t
ing
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added notes
on mdp disre
parameters
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
distance r
e
straint ens
e
m
ble
a
veragin
g
is no longer
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
B
erk Hess
fixed bu
g
in e
n
um parsing error
message
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added V
V
param
e
ters to md
p
_opt
.
ht
m
l
commit
|
commitdiff
|
tree
2010-06-02
Berk Hess
fixed
m
o
re Gr
o
mos atom typ
e
n
ame case
s
commit
|
commitdiff
|
tree
2010-06-01
B
er
k
Hess
cl
e
aner fix for
a
tom type cas
e
issue with GB para
m
eters
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
f
i
x
e
d atom type case issue
w
ith GB para
m
eters
commit
|
commitdiff
|
tree
2010-06-01
B
e
r
k
Hess
fixed two
G
B bugs
commit
|
commitdiff
|
tree
2010-05-19
Berk Hess
fixed mdrun unwantingl
y
m
odifying nstene
r
gy and ns
t
log
commit
|
commitdiff
|
tree
2010-05-18
Ber
k
H
e
s
s
implement
S
S
E
exp calc
u
l
ation for
s
olve_pme
commit
|
commitdiff
|
tree
2010-05-17
Berk
H
ess
fixe
d
som
e
g
e
n
born include
f
i
le de
t
ails
commit
|
commitdiff
|
tree
2010-05-17
Berk Hess
reor
d
ered p
m
e_solv
e
_yzx a
r
guments
commit
|
commitdiff
|
tree
2010-05-14
Be
r
k H
e
ss
minor p
m
e_solve virial optimizatio
n
commit
|
commitdiff
|
tree
2010-05-14
Berk Hess
fi
x
e
d seg
v
with mdrun -np
m
e 1
commit
|
commitdiff
|
tree
2010-05-12
Berk Hess
fixe
d
case of
a
tom types in the Gromos force fields
commit
|
commitdiff
|
tree
2010-05-12
Berk Hess
corrected pdb
2
g
m
x for
c
e
f
iel
d
com
m
e
n
ts
commit
|
commitdiff
|
tree
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