Dear gmx-users, Is it true that mdrun (3.3.1) should not write broken molecules under any circumstances? If the .xtc output contains broken molecules, should one be worried?
The molecules in my .xtc file are whole for the most of the time, but at some frames one or two are broken such that parts of the molecule are on opposite sides of the periodic box. I checked this with gmxdump and a short code of my own. Also, I was not able to make the molecules whole again with any of the -pbc options in trjconv. The molecules in the initial configuration are whole and I cannot see any reason for this. Best Regards, Perttu Niemela Helsinki Univ. Tech. Finland _______________________________________________ gmx-users mailing list [email protected] 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
