Hello,<br><br>Yes i did that. but qualitatively i did not see any such clashes.<br>But i do not know how to quantify it by calculations. <br><br>Thank you<br>with regards<br>Kavya<br><div class="gmail_quote">On Mon, Sep 26, 2011 at 5:51 PM, Sarath Chandra Dantu <span dir="ltr"><<a href="mailto:dsarath@gwdg.de">dsarath@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
> Hello again,<br>
><br>
> I centered it and then did the calculation again for minimum image<br>
> distance<br>
> but still it showed the same graph as without centering. I tried<br>
> visualising<br>
> it<br>
> using vmd but could not see any such clashes. since I am new to vmd<br>
> I do not know whether it is possible to calculate such clashes if at all<br>
> in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?<br>
><br>
<br>
</div>In VMD go to graphics then representations and select periodic. In<br>
periodic by clicking on +/- of each axis you can check if your protein<br>
bumps into itself.<br>
<br>
Best,<br>
<br>
Sarath<br>
<div><div></div><div class="h5"><br>
> Thank you<br>
> With regards<br>
> Kavya<br>
><br>
> On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
><br>
>> Thanks.<br>
>><br>
>><br>
>> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
>> wrote:<br>
>><br>
>>><br>
>>><br>
>>> Kavyashree M wrote:<br>
>>><br>
>>>> Dear users,<br>
>>>><br>
>>>> I was trying to simulate a protein dimer covalently bond with<br>
>>>> a disulphide bond (230+230 aa long). I used usual protocol<br>
>>>> as used for simulation of a monomeric protein, using gromacs-<br>
>>>> 4.5.3, dodecahedron box, tip4p water model and protein to<br>
>>>> box distance of 1 (-d in editconf). In the middle of the simulation<br>
>>>> when i checked for minimum image violation there was huge<br>
>>>> clashes. I am extremely sorry I have been asking regarding this<br>
>>>> many times but in this it is a dimer and I am not sure what mistake<br>
>>>> I have done because this happened while simulating another dimer<br>
>>>> also though not sever. Hence I seek some guidance from this<br>
>>>> community regarding the problem. I attach the graph herewith.<br>
>>>> Kindly help. Let me know if I need to give any other information.<br>
>>>><br>
>>>><br>
>>> Please see my post from yesterday for a more detailed reply to this<br>
>>> exact<br>
>>> same type of question. I am beginning to suspect there's a problem<br>
>>> with<br>
>>> g_mindist, but I have no solid evidence for that claim, just a hunch.<br>
>>> It<br>
>>> looks like your protein crosses a periodic boundary and that messes up<br>
>>> the<br>
>>> calculation. Please center the protein in the box with trjconv -center<br>
>>> and<br>
>>> re-analyze to see if there are any differences.<br>
>>><br>
>>> -Justin<br>
>>><br>
>>> --<br>
>>> ==============================**==========<br>
>>><br>
>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>
>>> ICTAS Doctoral Scholar<br>
>>> MILES-IGERT Trainee<br>
>>> Department of Biochemistry<br>
>>> Virginia Tech<br>
>>> Blacksburg, VA<br>
>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
</div></div>>>> <a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>**<a href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a><<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br>
<div class="im">>>><br>
>>> ==============================**==========<br>
>>> --<br>
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</div>>>> Support/Mailing_Lists/Search<<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>>before<br>
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> --<br>
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<br>
<br>
</div>--------------------<br>
Sarath Chandra Dantu<br>
Computational Biomolecular Chemistry<br>
Max Planck Institute of Biophysical Chemistry<br>
Am Fassberg 11,<br>
Gottingen<br>
37077<br>
Germany<br>
<br>
Email: <a href="mailto:dsarath@gwdg.de">dsarath@gwdg.de</a><br>
Tel: <a href="tel:%2B%2B49-551-201-2320" value="+495512012320">++49-551-201-2320</a><br>
Fax: <a href="tel:%2B%2B49-551-201-2302" value="+495512012302">++49-551-201-2302</a><br>
<div><div></div><div class="h5"><br>
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