Thanks, Mark I am so sorry about my failure to describe my problem clearly. My problem is that while I was doing EM with that infinite system, the Fmax was unreasonably large (~1e4). But just now, I changed the pbc=xyz to pbc=full in my em.mdp file, then it is OK now. So I have a new question now: as the pbc=full has never been mentioned in GROMACS 3.3 manual, what is the difference between pbc=full and pbc=xyz?
I have checked the example of CNT on the website you mentioned. I do not use x2top in my simulation, because I generate the input .gro and .itp files directly with other programs. I manually add the topology among atoms on the neighboring edges of graphene and its image. But the pbc=full mentioned in that example is very helpful. Thanks for your suggestion! silvester.thu 2008-05-15 发件人： Mark Abraham 发送时间： 2008-05-15 10:29:49 收件人： Discussion list for GROMACS users 抄送： 主题： Re: [gmx-users] how to build the input files of an infinite system 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 [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
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