[gmx-users] Dimer simulation problem

[Sarath Chandra Dantu]

> 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