On Mon, Apr 8, 2013 at 2:00 PM, fatemeh ramezani fr_...@yahoo.com wrote:
Dear all
I am simulating gold nanoparticle interaction with 10 aminoacids.Two
amino acids have been far from the nanoparticleafter 2000 steps.
Now, Can I change after2000 steps, the position of these 2 aminoacids in
PDP file and then continue the simulation?
I doubt that would be stable. You've taken a trajectory that has run for
some amount of time, seriously perturbed it, then you hope to continue it?
You're better off starting a new simulation altogether. Also realize that
2000 steps, irrespective of what the timestep is, is extremely short.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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