[gmx-users] Freeze group atoms changing position
jalemkul at vt.edu
Thu Oct 25 16:27:46 CEST 2012
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?
> On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul <jalemkul at 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
>> 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
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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