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

[Justin Lemkul]

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

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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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