[gmx-users] How to check if one protein broke into fragments during MD?
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
> 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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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