Thank you for your help,
using the CPU code, I didn't get any error: the potential energy lowered a
lot on the first steps and the density increased.
But now I have a different problem: I started the pH-REMD and they are
incredibly slow! Almost stuck.
I did this calculation on the system without membrane (32000 atoms) and I
got 1.19 ns/day on 12 nodes (144 cores in total) for 12 pH-REMD.
I used the same input, and the same hardware for the system WITH membrane
(41000 atoms) and I'm getting 78 ps in the last 24 hours. The only things I
changed are the modules I loaded, choosing gcc49 instead of gcc47 and
upgrading to python 2.7.11. Here is the input for pH1:
&cntrl
imin=0, ! No minimization
irest=1, ! Restart the simulation
ntx=5, ! Coordinates and velocities from coordinate file
ntxo=2, ! Format of the final coordinates NetCDF
ntpr=1000, ! Every ntpr steps, energy is printed
ntwx=1000, ! Every ntwx steps, the coordinates are written
nstlim=100, ! Number of steps between exchange attempts
dt=0.002, ! time step in ps
ntt=3, ! Langevin dynamics
tempi=300, ! Initial temperature
temp0=300, ! Reference temperature
gamma_ln=5.0, ! collision frequency
ig=-1, ! random seed
ntc=2, ! SHAKE bonds involving hydrogen are constrained
ntf=2, ! bond interactions involving H-atoms omitted
cut=8, ! nonbonded cutoff
iwrap=1, ! restart coordinate and trajectory files "wrapped" into a
primary box
ioutfm=1, ! Binary NetCDF trajectory
icnstph=2, ! CpHMD run in explicit solvent
ntcnstph=50, ! number of steps between attempting protonation state
changes
solvph=1, ! solvent pH
ntrelax=100, ! number of solvent relaxation steps
saltcon=0.1, ! salt concentration for the GB calculations
numexchg=10000, ! number of times to attempt exchanging
ntwr=10000, ! Every ntwr steps, the restrt file is written
/
Do you have any idea of the reason of this slowness? Indeed, equilibrating
the system using the mdin give by Jason on his wikidot tutorial, I got 15
ns/day on 2 nodes (24 cores).
Elisa
On Fri, Sep 30, 2016 at 2:06 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Sep 30, 2016, at 7:42 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
> >
> > Thank you Jason and David,
> >
> > I used the inputs at
> > http://jswails.wikidot.com/explicit-solvent-constant-ph-md; anyway,
> even if
> > the minimization and heating look fine, during the equilibration I get:
> >
> > ERROR: Calculation halted. Periodic box dimensions have changed too much
> > from their initial values.
> > Your system density has likely changed by a large amount, probably from
> > starting the simulation from a structure a long way from equilibrium.
> >
> > [Although this error can also occur if the simulation has blown up for
> > some reason]
> >
> > The GPU code does not automatically reorganize grid cells and thus you
> > will need to restart the calculation from the previous restart file.
> > This will generate new grid cells and allow the calculation to continue.
> > It may be necessary to repeat this restarting multiple times if your
> > system
> > is a long way from an equilibrated density.
> >
> > Alternatively you can run with the CPU code until the density has
> > converged
> > and then switch back to the GPU code.
> >
> > I don't really get what "you will need to restart the calculation from
> the
> > previous restart file" means..because what I understand is either
> "restart
> > from the heat.rst7", which of course does not make sense, or "restart
> from
> > the equil.rst7", which, in my case is unfortunately empty, since the
> error
> > occurs almost at the beginning of my simulation.
> >
> > Should I just switch to the CPU code? Or there is some other problem
> (and a
> > solution :) )?
>
> It may have blown up. If it dies almost immediately on the GPU, I suggest
> trying with the CPU and see if you get a more sensible error message.
>
> HTH,
> Jason
>
> >
> > Elisa
> >
> > On Thu, Sep 29, 2016 at 8:53 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >>> On Wed, Sep 28, 2016, Elisa Pieri wrote:
> >>>
> >>> I have a PDB containing a protein inserted in a membrane, plus two
> water
> >>> layers, yielding a "cubic" unit. Here the tleap input I used to get the
> >>> parameters:
> >>>
> >>> source leaprc.constphRET (<-- a customized leaprc for the cromophore)
> >>> source leaprc.lipid14
> >>> loadAmberParams frcmod.ionsjc_tip3p
> >>> monomer = loadPDB monomer.pdb
> >>> setBox monomer "vdw"
> >>
> >> Are you sure you want this command? Don't you already know the size of
> the
> >> box to use? If so, replace the above with this:
> >>
> >> set monomer box { a b c}
> >>
> >> where a b c are the sizes of the box in your model. Then, as Jason
> said,
> >> use periodic boundary conditions at all stages of subsequent
> calculations.
> >>
> >> ....good luck....dac
> >>
> >>
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Received on Sun Oct 02 2016 - 11:30:02 PDT
