[gmx-users] Freeze group atoms changing position

Alex Marshall amarsh59 at uwo.ca
Thu Oct 25 15:59:14 CEST 2012


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.

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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-- 
Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario



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