silvester.thu wrote: > Hello everyone, > > I am working on a simulation of an infinite system but I do not know how > to build its periodic boundary conditions in GROMACS. My system is a > graphene that is infinite on a certain direction. Surely I can not > generate an infinitely large graphene for input. So I want to make a > finite graphene to repeat along a certain direction in order to > approximate the "infinite" one (e.g: spread the finite graphene from > left to right). But I do not know the technical details. Anyone have > experience on this kind of problems?
Yes. You can probably adapt the advice here http://wiki.gromacs.org/index.php/Carbon_Nanotube to your needs. > I have tried to use the PBC in GROMACS, and add the bonds, angles and > dihedrals between atoms on the left edge and atoms on the right edge and > make the size of box to be just the same as the sum of length of C-C > bond and the width(the distance from the left edge to the right edge) of > graphene. But it did not work. > > Anyone can give me some advice? It will be very helpful. Describing failure with "It did not work" makes it impossible for us to give free advice at a rate that is worth our time. A detailed description of what you did and what happened is almost always much more valuable and a better use of everybody's time than the alternative :-) See the advice here http://wiki.gromacs.org/index.php/Support Mark _______________________________________________ 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
