[gmx-users] Minimum periodic distance

[Kavyashree M]

Hello Sir,

  Thanks for your reply sir. I will check to it.

With regards
M. Kavyashree

On Mon, May 30, 2011 at 4:59 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Kavya,
>
> There is no way to correct for such things afterwards. But I would
> guess it's not much of a problem in your case. If a situation with a
> short distance is only transient, it is unlikely to affect the
> simulation. On the other hand, you may have secondary, indirect
> effects due to water ordering. Whether that is problematic in your
> case is something you'll have to assess yourself.
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 30, 2011 at 12:24 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
> > Hello Sir,
> >
> > The difference between the rcolumb (1.4nm) and minimum image distance
> > that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine
> > residues (1.39714nm) is 0.00286nm = 0.0286Ang,
> > Since this distance is smaller than bond distance between hydrogen and
> > nitrogen which is ~1.0Ang, So will this effect the results of the
> > simulations?
> > Kindly let me know whether I need to redo the simulation again? or is
> there
> > any way to correct this or can it be ignored?
> >
> > Thanking you
> > With regards
> > M. Kavyashree
> >
> >
> > On Mon, May 30, 2011 at 10:36 AM, Kavyashree M <hmkvsri at gmail.com>
> wrote:
> >>
> >> Hello sir,
> >>
> >> I had used a dodecahedron cell for simulation. I have run
> >> the simulation for 100ns, did you man I have to restart the
> >> simulation again?
> >>
> >> Thanking you
> >> Kavya
> >>
> >> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> >> wrote:
> >>>
> >>> Hi Kavya,
> >>>
> >>> > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
> >>> > between atoms 2062 and 3688"
> >>> > where 2062 is a protein atom and 21824 is a water molecule.
> >>>
> >>> 21824 is the time in ps at which the two atoms indicated, 2062 and
> >>> 3688, are at the short distance given. You can dump the frame with
> >>> trjconv and have a look. Probably your molecule stretched, or you
> >>> solvated in a rectangular box and the protein rotated. In the first
> >>> case, set a larger distance, in the second, use a rhombic
> >>> dodecahedron.
> >>>
> >>> Cheers,
> >>>
> >>> Tsjerk
> >>>
> >>>
> >>> --
> >>> Tsjerk A. Wassenaar, Ph.D.
> >>>
> >>> post-doctoral researcher
> >>> Molecular Dynamics Group
> >>> * Groningen Institute for Biomolecular Research and Biotechnology
> >>> * Zernike Institute for Advanced Materials
> >>> University of Groningen
> >>> The Netherlands
> >>> --
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> >
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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