[gmx-users] Dimer simulation problem

[Kavyashree M]

Hello,

Yes i did that. but qualitatively i did not see any such clashes.
But i do not know how to quantify it by calculations.

Thank you
with regards
Kavya
On Mon, Sep 26, 2011 at 5:51 PM, Sarath Chandra Dantu <dsarath at gwdg.de>wrote:

>
> > Hello again,
> >
> > I centered it and then did the calculation again for minimum image
> > distance
> > but still it showed the same graph as without centering. I tried
> > visualising
> > it
> > using vmd but could not see any such clashes. since I am new to vmd
> > I do not know whether it is possible to calculate such clashes if at all
> > in vmd? I am using dodecahedron box. can it be visualised as it is in
> vmd?
> >
>
> In VMD go to graphics then representations and select periodic. In
> periodic by clicking on +/- of each axis you can check if your protein
> bumps into itself.
>
> Best,
>
> Sarath
>
> > Thank you
> > With regards
> > Kavya
> >
> > On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
> >
> >> Thanks.
> >>
> >>
> >> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <jalemkul at vt.edu>
> >> wrote:
> >>
> >>>
> >>>
> >>> Kavyashree M wrote:
> >>>
> >>>> Dear users,
> >>>>
> >>>> I was trying to simulate a protein dimer covalently bond with
> >>>> a disulphide bond (230+230 aa long). I used usual protocol
> >>>> as used for simulation of a monomeric protein, using gromacs-
> >>>> 4.5.3, dodecahedron box, tip4p water model and protein to
> >>>> box distance of 1 (-d in editconf). In the middle of the simulation
> >>>> when i checked for minimum image violation there was huge
> >>>> clashes. I am extremely sorry I have been asking regarding this
> >>>> many times but in this it is a dimer and I am not sure what mistake
> >>>> I have done because this happened while simulating another dimer
> >>>> also though not sever. Hence I seek some guidance from this
> >>>> community regarding the problem. I attach the graph herewith.
> >>>> Kindly help. Let me know if I need to give any other information.
> >>>>
> >>>>
> >>> Please see my post from yesterday for a more detailed reply to this
> >>> exact
> >>> same type of question.  I am beginning to suspect there's a problem
> >>> with
> >>> g_mindist, but I have no solid evidence for that claim, just a hunch.
> >>> It
> >>> looks like your protein crosses a periodic boundary and that messes up
> >>> the
> >>> calculation.  Please center the protein in the box with trjconv -center
> >>> and
> >>> re-analyze to see if there are any differences.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==============================**==========
> >>>
> >>> Justin A. Lemkul
> >>> Ph.D. Candidate
> >>> ICTAS Doctoral Scholar
> >>> MILES-IGERT Trainee
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>>
> >>> ==============================**==========
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>
> --------------------
> Sarath Chandra Dantu
> Computational Biomolecular Chemistry
> Max Planck Institute of Biophysical Chemistry
> Am Fassberg 11,
> Gottingen
> 37077
> Germany
>
> Email: dsarath at gwdg.de
> Tel: ++49-551-201-2320
> Fax: ++49-551-201-2302
>
>
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