[gmx-users] Dimer simulation problem

Kavyashree M hmkvsri at gmail.com
Wed Sep 21 13:42:31 CEST 2011


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
> 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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