Hi I simulate a hexa-meric protein (443*6=2658 residues with about 90000 water) Especially, I'm interested in water behavior around the protein.
The 1ns simulation is finished normally, but trjconv produces abnormal structure. For example, the protein go outside my waterbox, water molecules are diverse abnormally...etc. I try various options: trjconv -s full.tpr -f full.trr -o full.xtc -pbc nojump trjconv -s full.tpr -f full.trr -o full.xtc -pbc cluster trjconv -s full.tpr -f full.trr -o full.xtc -fit rot (select 1(thus protein) for fitting group) And, I watch full.xtc using VMD, but they are strange in all cases. For your information, I use cubic periodic boundary condition. Please suggest me. Greetings, Tomoshi _______________________________________________ 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
