Hi I am doing a 5 peptide simulation in a 6nm box. Now to check the correctness of my simulation i m calculating the minimum periodic distance using g_mindist to find out the distance between molecule and its periodic images.Following is the command i have used
g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg For the selection criteria i have used c-alpha atom of peptide 1. It is giving me the minimum distance of 6nm as expected but how can i see the maximum distance because by applying -max option also i am getting the same result 1. g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg Select a group: 19 Selected 19: 'c-alpha-gly1' Reading frame 16600 time 8300.000 The shortest periodic distance is 6 (nm) at time 0 (ps) this is the part of output mindist.xvg 0 6.000 0.000 6.000 6.000 6.000 0.5 6.000 0.000 6.000 6.000 6.000 1 6.000 0.000 6.000 6.000 6.000 1.5 6.000 0.000 6.000 6.000 6.000 2 6.000 0.000 6.000 6.000 6.000 2.5 6.000 0.000 6.000 6.000 6.000 3 6.000 0.000 6.000 6.000 6.000 2. g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg -max Select a group: 19 Selected 19: 'c-alpha-gly1' Reading frame 16610 time 8300.000 The shortest periodic distance is 6 (nm) at time 0 (ps) The part of output mindist.xvg 0 6.000 0.000 6.000 6.000 6.000 0.5 6.000 0.000 6.000 6.000 6.000 1 6.000 0.000 6.000 6.000 6.000 1.5 6.000 0.000 6.000 6.000 6.000 2 6.000 0.000 6.000 6.000 6.000 2.5 6.000 0.000 6.000 6.000 6.000 3 6.000 0.000 6.000 6.000 6.000 The minimum distance is 6nm and it is exactly what is expected but there should also be distances more than 6nm (considering 26 periodic images). I don't know how to get that. Also i want to ask one more thing what is "maximum internal distance " which is probably indicated by the third column of mindist.xvg output. Thanks Regards Alka _______________________________________________ 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