It will diffuse indefinitely. The problem with the PDB format (which is
really the problem with the ASCII restart format, as they both overflow
outside of (-1000, +10000) is that the number will show up as ******** and
then the next simulation segment to start will fail. The way to avoid this
is to set ioutfm=1, which I think may be the default, to get binary restart
files and trajectory coordinates.
As for diffusion in a GB simulation, there is code in there to reset the
positions of your system as a whole to the origin periodically. You should
think in detail about what you are doing.
Dave
On Tue, Jul 23, 2019 at 3:23 PM Mohammad Hassan Khatami <
MohammadHassan.Khatami.uoit.ca> wrote:
> Thanks David for your reply.
> Just out of curiosity, if I have a small methane (or any other particle or
> ions) in an implicit water, will it diffuse until it reaches to the
> limitation of XYZ in pdb format?
> Mohammad
>
> > On Jul 23, 2019, at 2:49 PM, David Cerutti <dscerutti.gmail.com> wrote:
> >
> > I don't think we handle implicit solvent and periodic boundary conditions
> > at the same time. For a system that large, implicit solvent (the way we
> > implement it) would be much slower than explicit solvent, anyway, and the
> > consensus is that implicit solvent is not as accurate. A large speedup
> and
> > sampling capability are needed to justify implicit solvent calculations,
> > although there are cases where that is true. CHARMM has implemented
> > implicit solvent membranes, but in those cases the membrane itself is a
> > different dielectric regime, another form of implicit solvation amidst
> the
> > implicit
> > water.
> >
> > DSC
> >
> >
> > On Tue, Jul 23, 2019 at 2:10 PM Mohammad Hassan Khatami <
> > MohammadHassan.Khatami.uoit.ca> wrote:
> >
> >> Hi everyone!
> >> I am trying to run simulations of lipid membrane in an implicit solvent.
> >> However, I am unable to define a box for the implicit solvent
> simulations.
> >> Is there anyway around it?
> >> Best,
> >> Mohammad
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Received on Tue Jul 23 2019 - 13:00:02 PDT
