On 10/24/12 3:17 PM, Alex Marshall wrote:
Hi all,
I'm simulating a system of two reservoirs connected by a carbon nanotube.
The reservoir wall atoms and carbon nanotube atoms are held in place using
freeze groups at all times. I'm currently equilibrating the reservoirs
separately by also freezing the water inside the nanotube, but after 20 ns
two of the frozen water molecules have jumped outside of the nanotube into
a supposedly inaccessible region. What could cause this? Should I be
worried?
I would be. Frozen groups aren't supposed to move at all. Verify that the
problematic water molecules are indeed contained within whatever frozen group(s)
you have assigned in the .mdp file. Otherwise, there's no immediate
explanation, especially since other frozen atoms are staying frozen.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* 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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
