[gmx-users] large radius problem

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 9 13:18:33 CEST 2012

On 7/9/12 7:09 AM, siddhant jain wrote:
> I was performing simulations on urea unfolding of protein. I performed
> one set of simulation for 50 ns with a velocity (set by gen_seed) and
> it went fine.
> Now when I am doing simulation using a different gen_seed from 10 to
> 20 ns many long bonds are formed. I could visualize them in vmd.
> Subsequently rmsd and radius of gyration plots also show the large
> change. But,  energy is almost constant during the whole time period.
> Also after 20 ns this problem goes by itself and all bonds become
> normal. Why it could be so and how could I correct it. These bonds are
> so long that radius of gyration changes from 1.2 nm to 3.5 nm.

That sounds like a PBC issue to me.




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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