[gmx-users] Dimer simulation problem

[Justin A. Lemkul]

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

-- 
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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

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