Hi all, We found some problems in using g_dist or g_minidist to calculate distance in some PBC condition, dodecahedron The output is as followed:
Back Off! I just backed up mindist.xvg to ./#mindist.xvg.2# 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} Can not fix pbc. The input pdb is like this REMARK GENERATED BY TRJCONV TITLE Protein in water t= 394.00003 REMARK THIS IS A SIMULATION BOX CRYST1 64.653 64.689 64.375 70.32 109.46 70.63 P 1 1 MODEL 0 ATOM 201 C1' RA 7 13.130 -2.870 23.080 1.00 0.00 ATOM 553 O4' RU 18 44.730 54.920 28.830 1.00 0.00 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 Milan Melichercik Sent: Wednesday, August 23, 2006 7:50 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein in bilayer Dňa St 23. August 2006 13:42 mahbubeh zarrabi napísal: > dear itamar > where is adress make-hole site? > thanks 3rd record on following page http://www.gromacs.org/contributed_by_users/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,5/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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