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

Vitaly Chaban vvchaban at gmail.com
Sat Jul 10 09:57:43 CEST 2010

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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