Hi everyone,
I have been running AMBER simulations of a transmembrane helix inserted
into a POPC bilayer. My original dimensions for the periodic box were:
88.48 x 84.58 x 83.25; However, after running the pmemd.cuda version of
AMBER18 for around 1 microsecond, the dimensions have changed to 63.43 x
139.09 x 81.99.
My systems are set with anisotropic settings (npt=2) and Monte-Carlo
barostat (ntb=2) - same as in the lipid14 tutorial. In addition, I have
iwrap=1 so that it wraps on itself. Can anyone tell me why this
is happening and how can i fix it? (my production.in file is detailed
below).
I have read other mailing threads talking about the same issue, and
normally, as long as the density of the box doesn't change much, is
supposed to be okay but my peptide is basically touching both sides of my
box due to the shrinkage of the x-dimension, and i'm worried it's going to
start interacting with itself.
In addition, my production runs tend to stop after a few ns (around
150-200ns) due to the following error:
* ERROR: Calculation halted. Periodic box dimensions have changed too much
from their initial values.*
And I'm wondering if anyone can explain why is that happening, since all i
can find makes reference to the statement described above.
Thank you in advance.
*Lipid production 303K 125ns &cntrl imin=0, ! Molecular dynamics
ntx=5, ! Positions and velocities read formatted irest=1,
! Restart calculation ntc=2, ! SHAKE on for bonds with
hydrogen ntf=2, ! No force evaluation for bonds with hydrogen
tol=0.0000001, ! SHAKE tolerance nstlim=150000000, ! Number of MD steps
ntt=3, ! Langevin thermostat gamma_ln=1.0, ! Collision
frequency for thermostat temp0=310.0, ! Simulation temperature (K)
ntpr=5000, ! Print to mdout every ntpr steps ntwr=50000, ! Write
a restart file every ntwr steps ntwx=50000, ! Write to trajectory
file every ntwc steps dt=0.002, ! Timestep (ps) iwrap=1 ! wrap
atoms around box ig=-1, ! Random seed for Langevin thermostat
ntb=2, ! Constant pressure periodic boundary conditions ntp=2,
! Anisotropic pressure coupling cut=10.0, ! Nonbonded
cutoff (Angstroms) ioutfm=1, ! Write binary NetCDF trajectory
ntxo=2, ! Write binary restart file /*
Violetta Burns
PhD student
Mertz Group
WVU Department of chemistry
"*Every great and deep difficulty bears in itself its own solution. It
forces us to change our thinking in order to find it." - Niels Bohr*
*“You do not really understand something unless you can explain it to your
grandmother.” - Albert Einstein*
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Received on Fri Jun 28 2019 - 17:30:03 PDT
