[gmx-users] Freeze group atoms changing position

[Justin Lemkul]

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 <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
>>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
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>

-- 
========================================

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

========================================