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

shuai shuai banshuai at gmail.com
Sat Jul 10 23:53:09 CEST 2010

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.


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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