Well, the way you should follow depends much on what you want to calculate exactly.
Of course, any artificial constraint is bad. > It is even worst! Removing the center of mass motion of your protein > alone as suggested is an aberration and should never be done! > That doesn't necessarily "fix" the "problem". > Which position of the > protein is taken as a reference depends on the position of the first > atom. Gromacs wants to have the first atom of a molecule in the > rectangular unit cell at the origin. Even if you set comm removal for > the group, the initial orientation and/or conformational changes may > cause the first atom to jump over the boundaries. > > Whatever the case, everyone doing MD simulations should be aware of > periodic boundary conditions. There is no "outside of the box". -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svobody sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban _______________________________________________ gmx-users mailing list [email protected] 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
