[gmx-users] Dimer simulation problem

[Mark Abraham]

On 26/09/2011 10:02 PM, Kavyashree M 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. 

Have you followed the kind of workflow suggested here? 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

> 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?

Yes, one can be visualized, but some preparation with trjconv -ur 
compact (as hinted at in trjconv -h) is a good idea.

Mark

>
> Thank you
> With regards
> Kavya
>
> On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <hmkvsri at gmail.com 
> <mailto:hmkvsri at gmail.com>> wrote:
>
>     Thanks.
>
>
>     On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <jalemkul at vt.edu
>     <mailto: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 <http://vt.edu> | (540) 231-9080
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>         ========================================
>         -- 
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