Amber users,
I'm using Amber20 with PLUMED 2.8.0 to do umbrella sampling along a custom
CV. Everything is going fine, except on rare occasions the PLUMED output
files will have some serious formatting errors. A couple recent examples:
A missing newline:
...
18.735000 -9.940796
18.736000 -9.89812 18.776000 -10.107412
18.777000 -10.098970
18.778000 -10.053000
...
Overwriting the end of one line with the next:
...
18.406000 -10.088869
18.407000 -10.08718.368000 -9.975116
18.369000 -10.082246
...
Asking around among some colleagues who regularly use PLUMED with Gromacs,
they don't report having ever encountered something like this, so I'm
guessing it's Amber-specific. Does anyone have any suggestions to prevent
this from happening?
An input file, for completeness:
Umbrella sampling
&cntrl
imin =0,
irest=0,
ntx=1,
ntxo=1,
nstlim=250000,
dt=0.001,
ntt=2,
tempi=310.0,
temp0=310.0,
vrand=1000,
ntp=1,
taup=2.0,
ntb=2,
ntc=2,
ntf=2,
ntwx=250,
ntpr=250,
ntwr=250,
ntwv=-1
cut=8.0,
iwrap=0,
ifqnt=1,
igb=0,
nmropt=1,
ig=-1,
plumed=1,
plumedfile='plumed.in',
/
&qmmm
qmmask=".1908-1912,2532-2537,2983-2993,3833-3886",
qmcharge=-1,
qm_theory="DFTB3",
qm_ewald=1,
qmshake=0,
qmcut=8.0,
/
&wt
type="END",
&end
DISANG=additional_restraints.DISANG
And here's the relevant bits of a representative plumed.in file:
...
restraint-rc: RESTRAINT ARG=RC KAPPA=100.0 AT=-9.75
PRINT ARG=RC FILE=rcwin_-9.75_1_us.dat
Thanks!
-Tucker Burgin
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Received on Wed Oct 12 2022 - 10:00:03 PDT
