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.
shuai 2010/7/10 Vitaly Chaban <vvcha...@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: > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php