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.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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