Dear Sir
Good Day !
Thanks for this very important piece of information !
I have replicated my unit cell by "PropPDB" only from the smallest side in
order to enlarge the super cell but not too much not to increase the
computational cost very much.
Regards
Hadeer
On Thu, Oct 15, 2015 at 1:59 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Oct 15, 2015 at 3:26 AM, Hadeer ELHabashy <
> hadeer.elhabashi.gmail.com> wrote:
>
> > Dear Sir
> >
> > wish you are fine !
> >
> > I need to run MD simulation on a small constant volume periodic box
> > containing only a crystal of a protein without any solvation. However,
> when
> > minimizing the structure, I had a problem with the cut of . the cut off
> > needed to be very small about 1 Angstrom and the minimization was not
> able
> > to run without higher or lower values of cut off .
>
>
> Then your box is too small to run simulations using the minimum image
> convention. Many bonds (especially between heavy atoms) have lengths
> larger than 1 Angstrom. This is a rather ridiculous cutoff, and I wouldn't
> expect any simulations employing it to actually work (it's certainly not
> tested). If your unit cell is too small for an 8 A cutoff, then you need
> to make your unit cell larger.
>
> There is no alternative within Amber (you would need a simulation package
> that *doesn't* use the minimum image convention, and would instead populate
> the pairlist with multiple images of the same atom if necessary, and I
> don't know of a single simulation package that behaves that way --
> certainly not any of the "mainstream" ones like Amber, CHARMM, GROMACS,
> OpenMM, LAMMPS, ...).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 15 2015 - 05:30:05 PDT
