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renamed amber LYP to LYS and changed names for water models in the rtp files
2010-07-26
Berk Hess
r
enamed
amber LYP t
o
LYS
a
nd changed na
m
es f
o
r water
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
rem
o
ved HOH from amb
e
r r
n
a
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added
missi
n
g
entri
e
s
for ambe
r
rna
.
hdb
commit
|
commitdiff
|
tree
2010-07-26
B
e
rk H
e
ss
c
le
a
ned up Am
b
er hdb's
and a
d
ded HO4
commit
|
commitdiff
|
tree
2010-07-26
B
erk Hess
re
n
ame
d
ato
m
types
f
r
o
m amber99_? etc
.
t
o
th
e
origin
a
l
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
fixed PME communi
c
a
tion range (no s
i
lent errors)
commit
|
commitdiff
|
tree
2010-07-26
B
erk
H
e
s
s
removed building
block RT f
r
om the
lists
i
n share/
t
op
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
added residue and atom renaming
f
or AMBER dna and r
n
a
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
a
dded DNA a
n
d
RNA to the pdb2gmx
.
arn format
commit
|
commitdiff
|
tree
2010-07-26
Be
r
k Hess
renamed O to O2
i
n amber rna
.
rtp
commit
|
commitdiff
|
tree
2010-07-26
Berk
H
ess
added natoms
_
fo
r
ce_c
o
ns
t
r to
t_forcerec
commit
|
commitdiff
|
tree
2010-07-26
Berk Hess
rena
m
ed
O to O2 in ambe
r
dna
.
rtp
commit
|
commitdiff
|
tree
2010-07-23
Berk
Hess
re
m
oved garba
g
e
from checkpoint
.
c
commit
|
commitdiff
|
tree
2010-07-23
Berk
Hess
fi
x
ed (rare) incorre
c
t residue number
s
whe
n
us
i
ng
g
mx_mtop_a
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Berk Hess
add
e
d o
p
e
nmm wrap
p
er RF para
m
eter checks
commit
|
commitdiff
|
tree
2010-07-19
Ber
k
Hess
minor update
to
t
he previos appending fix
commit
|
commitdiff
|
tree
2010-07-19
Berk Hess
f
ixe
d
mdrun append c
h
e
c
k when
requested outpu
t
file
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Berk
Hess
a
d
ded mdp pa
r
ameter
f
o
r FE dH tables
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
changed the d
e
f
aul
t
maximu
m
number of backups from
.
.
.
commit
|
commitdiff
|
tree
2010-07-05
Berk Hess
removed a lot of
slow
F
FT
gr
i
d sizes
f
ro
m
calc
_
grid
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Berk
H
ess
documen
t
ed pull c
o
sin
e
weighting
commit
|
commitdiff
|
tree
2010-06-28
Berk Hes
s
ren
a
med mdru
n
-cptnum to -cp
n
um
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
add
e
d mdrun -c
p
tn
u
m opt
i
o
n
to
k
eep
a
n
d numb
e
r checkpoints
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
reverted acc
i
denti
a
l change of tabangl
e
s in gro
m
pp
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
B
erk H
e
s
s
ad
d
ed include update
.
h to coupling
.
c
commit
|
commitdiff
|
tree
2010-06-28
Berk Hess
a
dded back const
t
o
gmx_sort
c
o
mpa
r
e
par
a
ms for
q
so
r
t
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
remov
e
d
obsolete
f
ftgrid co
d
e and di
s
a
bled PPP
M
with
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Berk Hess
changed pdb2gmx
wate
r
model
a
tom
c
o
u
nt detection
commit
|
commitdiff
|
tree
2010-06-24
B
e
rk Hess
impl
e
me
n
ted ns
t
e
ps=-1 for mdrun contin
u
ation and
t
pb
c
on
v
commit
|
commitdiff
|
tree
2010-06-24
Berk H
e
s
s
fi
x
ed sma
l
loc
.
h and smallo
c
.
c definitio
n
incon
s
i
s
tencies
commit
|
commitdiff
|
tree
2010-06-24
Berk Hes
s
M
e
rge b
r
anch 'master' of git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-23
Be
r
k Hess
removed
statusi
o
.
h
commit
|
commitdiff
|
tree
2010-06-23
Ber
k
He
s
s
fixed gmx_eneconv co
m
piler warnings
commit
|
commitdiff
|
tree
2010-06-23
Berk Hess
f
i
xed eneconv
-dt option temporarily
not
w
r
iting averages
commit
|
commitdiff
|
tree
2010-06-22
Berk Hess
corr
e
cted edr forma
t
issue
in
t
roduced t
o
day
commit
|
commitdiff
|
tree
2010-06-21
Ber
k
Hes
s
add gmx_qsort routine, sin
c
e glibc q
s
o
rt is not thr
e
adsafe
.
.
.
commit
|
commitdiff
|
tree
2010-06-21
Berk Hess
fix
e
d
t
yp
o
in fatal_er
r
or call
commit
|
commitdiff
|
tree
2010-06-18
Berk H
e
ss
n
ow mdrun does
n
ot write th
e
tr
r
file w
h
en
i
t would
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
Berk Hess
added
env
v
ar GMX_MAXBA
C
KUP
commit
|
commitdiff
|
tree
2010-06-17
Be
r
k
H
e
ss
fi
x
for th
e
previous
mdr
u
n -r
e
r
un commit
commit
|
commitdiff
|
tree
2010-06-17
B
e
rk H
e
ss
mdrun
-rerun now reads th
e
rer
u
n traj only on the master
.
.
.
commit
|
commitdiff
|
tree
2010-06-17
Berk He
s
s
minor update f
o
r previous replex bugfix
commit
|
commitdiff
|
tree
2010-06-17
B
erk Hess
f
i
x
ed
mdrun -
r
eru
n
giving
N
aN with dispcorr
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
a
d
de
d
water model se
l
ec
t
ion and lis
t
file t
o
pd
b
2
g
mx
commit
|
commitdiff
|
tree
2010-06-17
Berk
Hes
s
m
ad
e
a
s
e
par
a
t
e
t
ips3p
.
itp f
i
l
e
for CHARMM
commit
|
commitdiff
|
tree
2010-06-17
Berk Hess
Mer
g
e bra
n
c
h
'master' o
f
git@gi
t
.
g
r
omac
s
.
o
rg:
g
romacs
commit
|
commitdiff
|
tree
2010-06-16
B
e
rk He
s
s
adde
d
s
pce
t
o charmm27
commit
|
commitdiff
|
tree
2010-06-16
B
e
r
k
H
ess
fixe
d
MPI crash
w
h
en n
a
t_ho
m
e=0 in DD
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
restored the old order of
t
he m
d
ru
n
option and remove
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Berk He
s
s
replace
d
more gmx_fa
t
al by colle
c
tive calls in
DD
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
e
ss
fixed atom naming in encad c-termini
commit
|
commitdiff
|
tree
2010-06-16
Berk
H
ess
wi
t
h nsteps=-1 mdrun
now prints ns/day es
t
i
m
ate
commit
|
commitdiff
|
tree
2010-06-16
Berk Hess
added nsteps=-1 op
t
ion
to mdp_opt
.
html
commit
|
commitdiff
|
tree
2010-06-16
Berk
Hess
all energy
m
i
nimi
z
e
r
s now do
0
s
teps w
i
th nsteps=0
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
B
e
rk Hess
fixed incorrect pdb2
g
mx CYS2
to CYS ren
a
m
i
n
g
which
.
.
.
commit
|
commitdiff
|
tree
2010-06-15
Berk Hes
s
a
l
l
vsall loop
s
now trigge
r
pa
r
ticl
e
deco
m
p
o
sition
commit
|
commitdiff
|
tree
2010-06-15
Berk
H
ess
f
a
tal_
e
rror in the DD
i
nitial
i
zation n
o
w calls MP
I
_Fin
a
liz
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
B
e
rk Hess
added -c
w
d
option
to
pdb2gmx
commit
|
commitdiff
|
tree
2010-06-11
B
e
rk Hes
s
fixed mdrun counter resetting issue
s
commit
|
commitdiff
|
tree
2010-06-11
B
erk Hess
optimized the number o
f
threads
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
made DD work properly w
i
th all non
-
periodi
c
sys
t
em
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Berk Hess
added mo
r
e ex
p
l
a
nation t
o
idef
.
h
commit
|
commitdiff
|
tree
2010-06-10
Be
r
k
H
ess
fixed uniniti
a
lized
v
a
r
iable in do_md
commit
|
commitdiff
|
tree
2010-06-10
B
e
rk Hess
fixed particle
decomposit
i
o
n
l
o
ad
p
r
i
nt
commit
|
commitdiff
|
tree
2010-06-04
Berk
Hess
fix
e
d pdb2gmx messing up
coordinates when deleting
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added notes on
m
dp disre par
a
m
e
ters
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
distance
r
e
stra
i
nt ensemble averaging is no
l
o
nger
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
B
e
rk
H
ess
fix
e
d bug in enu
m
parsing
e
r
ror
m
essage
commit
|
commitdiff
|
tree
2010-06-03
Berk Hess
added
V
V parameters
to
m
dp_
o
pt
.
h
t
ml
commit
|
commitdiff
|
tree
2010-06-02
Berk Hess
fixed more
G
r
o
mo
s
ato
m
ty
p
e nam
e
c
a
ses
commit
|
commitdiff
|
tree
2010-06-01
Ber
k
H
e
ss
cleaner
fix fo
r
a
tom type case issue with GB par
a
mete
r
s
commit
|
commitdiff
|
tree
2010-06-01
Berk Hess
fi
x
ed
a
t
om type
c
a
se issue with GB param
e
ters
commit
|
commitdiff
|
tree
2010-06-01
B
e
rk Hess
fixed two GB bugs
commit
|
commitdiff
|
tree
2010-05-19
B
e
rk Hess
fixed mdrun un
w
antingly modifyi
n
g n
s
t
en
e
rgy and nstlog
commit
|
commitdiff
|
tree
2010-05-18
Be
r
k Hess
implement SSE
exp calculation fo
r
s
o
l
ve_pme
commit
|
commitdiff
|
tree
2010-05-17
Berk
Hess
fixed
some genborn incl
u
de file details
commit
|
commitdiff
|
tree
2010-05-17
Berk Hes
s
re
o
r
dered pme_solve_yzx a
r
gumen
t
s
commit
|
commitdiff
|
tree
2010-05-14
Berk Hes
s
mi
n
o
r
pme_solve virial
optimization
commit
|
commitdiff
|
tree
2010-05-14
Berk
H
e
ss
fixed segv with mdrun -npme 1
commit
|
commitdiff
|
tree
2010-05-12
Berk H
e
ss
fixed case of a
t
om
t
ypes in the G
r
omos force
fields
commit
|
commitdiff
|
tree
2010-05-12
B
erk Hess
co
r
re
c
ted p
d
b2
g
mx for
c
e field com
m
ents
commit
|
commitdiff
|
tree
2010-05-11
Berk
H
ess
m
ade atom types
c
ase sensitive
commit
|
commitdiff
|
tree
2010-05-11
Ber
k
He
s
s
fixed
b
ug in pdb2gm
x
hdb initialization
commit
|
commitdiff
|
tree
2010-05-11
B
e
rk Hess
a
d
ded
proper DNA and RNA
residue
r
ecognition
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
added prop
e
r DN
A
and
R
NA
r
es
i
due recognition
commit
|
commitdiff
|
tree
2010-05-11
B
e
rk Hess
fixed incorrec
t
pd
b
2gmx residue na
m
e matching with
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
fixed bug with pdb2gmx
and mult
i
ple rtp file
s
commit
|
commitdiff
|
tree
2010-05-11
Berk Hess
a
d
ded check for
sy
s
/time
.
h existe
n
ce
commit
|
commitdiff
|
tree
2010-05-11
Berk He
s
s
updated and fine-tuned the
coefficients for
t
h
e PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
B
e
rk Hess
removed
includ
e
of
c
omplex
.
h in ff
t
5d
.
h
commit
|
commitdiff
|
tree
2010-05-10
Berk
H
ess
fixed under
a
l
l
o
catio
n
in
g
mx_
f
ft_ini
t
_many_1d_
r
e
a
l
commit
|
commitdiff
|
tree
2010-05-10
Be
r
k Hess
fixed name
i
n gromos43a1
.
ff Makefile
.
am
commit
|
commitdiff
|
tree
2010-05-10
Berk H
e
ss
moved alcohol files
f
rom top to the force field
subdirectories
commit
|
commitdiff
|
tree
2010-05-10
B
erk Hess
moved alcoh
o
l file
s
from
t
op t
o
the
f
orce
field su
b
directori
e
s
commit
|
commitdiff
|
tree
2010-05-10
Berk Hess
c
o
mple
t
ion of
t
he pd
b
2gmx resid
u
e re
n
aming chan
g
e
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
changed inter
n
al Gr
o
macs naming of cys, his a
n
d ly
s
commit
|
commitdiff
|
tree
2010-05-07
Ber
k
Hess
adde
d
a column f
o
r single resi
d
ue c
h
a
i
n t
o
r2b
f
i
l
e
commit
|
commitdiff
|
tree
2010-05-07
Berk Hess
fixed segv in gro
m
pp when gmxcpp re
p
o
r
ts an
e
rror
commit
|
commitdiff
|
tree
2010-05-07
Ber
k
H
e
s
s
m
a
de
g
rompp c
h
ar
g
e warning less sens
i
tive to ro
u
nding
.
.
.
commit
|
commitdiff
|
tree
2010-05-07
B
e
r
k Hess
made PM
E
energ
y
a
nd vir
i
al calcula
t
i
on op
t
ional
commit
|
commitdiff
|
tree
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