Thanks Tsjerk, Probably because we use pressure coupling and the box size is deformed.
Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, May 16, 2007 12:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PBC problem Hi Yuguang, > Warning: Triclinic box is too skewed. > Box (3x3): > Box[ 0]={ 6.46530e+00, 0.00000e+00, 0.00000e+00} > Box[ 1]={ 2.14552e+00, 6.10274e+00, 0.00000e+00} > Box[ 2]={-2.14464e+00, 3.05200e+00, 5.24664e+00} This is not a rhombic dodecahedron. > CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1 This shows that the second vector is larger than the first, thus violating the gromacs rules for proper boxes (manual chapter 3; although it could be handled a bit more liberally, especially in the analysis tools). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php