Hi Paul,
From the manual page for Molecular Dynamics Simulation:
"Select model: The model of interest should be chosen by clicking to highlight its name in the list of models. All of the atoms for simulation should be included in this model; any other models will be ignored.” You can see that page by clicking the Help button on the tool dialog, or view the copy on our website: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html> Elaine
On Jun 7, 2017, at 11:23 AM, pbuscemi <pbuscemi@q.com> wrote:
Thanks Elaine,
Your assumptions were correct..and I apologize for the poor description.
If I were to open the two files as two models - surface and water - and select only water to run the simulation ( only water is active ) would the water know the surface was present ?
Paul