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.
>
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> *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
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>
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Received on Sat Jun 29 2019 - 00:00:01 PDT
