[gmx-users] can I change atom position after x steps
jalemkul at vt.edu
Mon Apr 8 20:02:58 CEST 2013
On Mon, Apr 8, 2013 at 2:00 PM, fatemeh ramezani <fr_750 at 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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