> > Dear all > I attach 8 carbonyl groups onto a > carbon nanotube (CNT). Each carbonyl group is considered as a residue named > "Car" and each carbon atom in the CNT is considered as a residue named > "Gr1". In the mdp file, the freezegrps are Gr1 and Car, and the freezedim > are Y Y Y Y Y Y. Does it mean that all the C in the CNT and C and O in the > carbonyl groups are fixed in three dimensions and they can not move in any > direction. However, when I made the energy minimization, the coordinates of > C and O in carbonyl groups changed. > How can I really fix the atoms? Look forward > for your suggestions! >
All the atoms which relate to your frozen groups should be non-movable during MD. >the coordinates of C and O in carbonyl groups changed. Only ones of CHO changed? And the CNT itself is nonmovable? Check your groups please. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
