[gmx-users] can I change atom position after x steps

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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