[gmx-users] Some molecules disconnected into many parts after EM

[Justin A. Lemkul]

VMD guesses bonds based on distances, so it is not necessarily very smart.

I have no idea why increasing the box causes the molecules to be displayed 
correctly, other than that VMD cannot deal with the periodicity correctly, as I 
implied before.  Causing all of the molecules to be within the unit cell may 
lead VMD to induce the desired visualization.

But in any case, bonds aren't broken and/or formed in classical MD so there is 
likely nothing to be concerned about.

-Justin

Yanmei Song wrote:
> Dear Justin:
> 
> Thanks for your message.
> 
> When I open the gro file using VMD it shows:
> 
> atom:1950
> bonds 1907
> residue:43
> 
> I was thinking the problem may not come from the artifact of 
> visualization. Since if the gro file is fine it should be like:
> 
> atom:1950
> bonds 1944
> residue:6
> 
> because I have 6 chains in the box.
> 
> This morning I found that it seems the problem was resolved by 
> increasing the box size. Why is that?
> 
> 
> On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Yanmei Song wrote:
> 
>         Dear users:
> 
>         I set up a 8nm cubic box with 6 long chain molecules. After EM,
>         there is no error message. However I found that in the gro file
>         by visualization, 2 of the chains has been split in many parts,
>         which means many bonds in the molecules disconnected. And also
>         the other 4 are good. I checked em.log and eveyting looks fine.
> 
>         Steepest Descents converged to machine precision in 1545 steps,
>         but did not reach the requested Fmax < 10.
>         Potential Energy  = -7.51461594735782e+03
>         Maximum force     =  2.66505909651672e+02 on atom 1256
>         Norm of force     =  9.84300153087768e+00
> 
>         Anyone knows how to solve the problem? Thanks in advance!
> 
> 
>     Probably an artifact of visualization, or otherwise periodic
>     boundary conditions:
> 
>     http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
> 
>     -Justin
> 
>         -- 
>         Yanmei Song
>         Department of Chemical Engineering
>         ASU
> 
> 
>         ------------------------------------------------------------------------
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     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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> 
> 
> 
> 
> -- 
> Yanmei Song
> Department of Chemical Engineering
> ASU

-- 
========================================

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

========================================