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

[Vitaly Chaban]

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: