Dear Chris,
Thank you for your response. I'll try the semi-anisotropic approach. thanks.
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*
On Sat, Jun 29, 2019 at 2:48 AM Chris Neale <candrewn.gmail.com> wrote:
> Dear Violetta:
>
> what you want is not anisotropic pressure coupling but semi-anisotropic
> pressure coupling where the X and Y are coupled together, independently
> from Z. Here is what I use for that:
>
> ! Constant pressure control. Note that ntp=3 requires barostat=1
>
> barostat=2, ! Berendsen... change to 2 for MC barostat
>
> ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/
> surften
>
> pres0=1.01325, ! Target external pressure, in bar
>
> taup=4, ! Berendsen coupling constant (ps)
>
> comp=45, ! compressibility
>
>
> ! Constant surface tension (needed for semi-isotropic scaling).
> Uncomment
>
> ! for this feature. csurften must be nonzero if ntp=3 above
>
> csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
>
> gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso
> scaling
>
> ninterface=2, ! Number of interfaces (2 for bilayer)
>
> On Fri, Jun 28, 2019 at 6:27 PM Violeta Burns Casamayor <
> vb0009.mix.wvu.edu>
> wrote:
>
> > 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*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jul 01 2019 - 10:30:02 PDT
