[gmx-users] Re: Frozen N2 in a very long tube

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 11 00:09:59 CEST 2010

shuai shuai wrote:
> Dear all,
> thanks for your suggestions. During this NVT simulation, I keep
> nanotube rigid. So the temperature should only couple to Nitrogen
> instead of the whole system as my original input file. I will try to
> couple temperature only to nitrogen to see whether this is the reason.
> Many thanks again, especially Dr. Vitaly Chaban.

This is not what has been suggested to you, nor does it sound terribly 
realistic.  How can one element of a system be controlled by a thermostat, and 
the other not?  If these two species interact (i.e. experience collisions), then 
it seems to me that they need to exchange energy in some way.

Note, too, that now two people have asked you about your charges on N2.  It 
seems like an odd physical model.  In the future, you would benefit from posting 
this information, as well as a complete .mdp file for what you're doing.


> shuai
> 2010/7/10 Vitaly Chaban <vvchaban at gmail.com>:
>> Dear Shuai:
>> Please try to couple temperature for nanotube and nitrogen separately.
>> BTW, what is your partial charge and how did you construct it?
>> Good luck!
>> Dr. Vitaly Chaban
>>> Recently I met a strong error from gromacs. Therefore I would like to know
>>> whether you have experienced the same thing or what is the reason for that.
>>> The system I simulated is nvt MD for N2 (with partial charge) diffusion in a
>>> long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a
>>> small cluster after a few ns. The weird thing is that I do not have
>>> such problem for either longer domain or short domain.  The input
>>> parameters are:
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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