[gmx-users] Re: DNA simulations

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 5 15:30:03 CEST 2012

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.



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.
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/DNA-simulations-tp4998988p4999100.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

More information about the gromacs.org_gmx-users mailing list