[gmx-users] Re: DNA simulations

[Tsjerk Wassenaar]

Uhmm, you remove particles, modify molecule types, and wonder whether
there is continuity in the trajectories?

Ah well, let's say you were to do a simulation and at some point t you
suddenly have some hydrogen atoms that have lost all interaction with
the system, and on top of that have the nature and charge of some
other atoms changed. In principle, you could say the trajectory
(position/momenta) is still continuous in that point.

Cheers,

Tsjerk

On Thu, Jul 5, 2012 at 2:53 PM, SatyaK <mail2mvskumar at yahoo.com> wrote:
>
>  Hello Tsjerk,
>
>  I was wondering, once we order the water molecules and place Oh radicals in
> the system,  do we loose the continuity of their trajectories when we run
> the simulations using Lammps?
>
>  With Regards,
>  Satya.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands