On 10/25/12 9:59 AM, Alex Marshall wrote:
Thanks Justin. I identified the offending waters using vmd (adding 1 to
resID and atom number since vmd starts counting at 0) and checked
confout.gro to make sure the coordinates matched up. I only have one group
for all frozen atoms in the system, and these guys are definitely in it.
Then I'm stumped. Freezing shouldn't partially work - either it does or
doesn't, and I've never seen anything like this. As a test, do simple position
restraints fare better?
-Justin
On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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