[gmx-users] How to check if one protein broke into fragments during MD?

Justin Lemkul jalemkul at vt.edu
Mon Jun 17 17:14:02 CEST 2013

On 6/17/13 11:00 AM, maggin wrote:
> Hi, all
> 1dx0.pdb during MD step at 19532ps are broken into 8 fragments, as VMD show
> about  bovin19532.gro
>    <http://gromacs.5086.x6.nabble.com/file/n5009221/aa.jpg>
> as picture shows that  at the bottom the number of protein is 8
> while when I use VMD to see md_0_1.gro the last structure of MD finished
> <http://gromacs.5086.x6.nabble.com/file/n5009221/bb.jpg>
> at the bottom the number of protein is 1
> So, it seems from last structure it can not tell if is this protein broken.
> Is there anyway to check if protein  is broken during MD?

By definition, bonds cannot break or form during MD.  Therefore, your protein 
can't possibly break apart.  What you're seeing is the effect of periodic 
boundaries.  In the trajectory, mdrun writes "broken" configurations that are 
easily accounted for using trjconv (see the manual).  For convenience, the final 
snapshot is always written such that it is properly rebuilt.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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