Dear Alex: Thank you very much for your reply, but I think I may not have expressed my doubts.
First, I multiplied a graphite unit cell in x y z three directions, then cut it to the size I needed, and carefully adjusted the carbon atoms at the edges to conform to the periodic boundary conditions. Therefore, there should be no problem in the way the graphite layers are stacked. Second, I dug a spherical hole in the graphite I got in the first step. As a result, each layer of graphite is clearly different. Based on your comments, I should create a top file for each layer of graphite using the x2top command alone. Actually I don't quite understand why I can't create a top file directly for the entire graphite? Finally, the main problem I encountered was that the graphite layers were separated from each other during the simulation and could not maintain the original configuration. I don't want to freeze the whole graphite, because then it is non-physical. Is there any way to fix the multi-layer graphite in addition to freezing? Thank you again for your reply! Kevin > -----Original Messages----- > From: Alex <nedoma...@gmail.com> > Sent Time: 2018-11-28 11:50:20 (Wednesday) > To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> > Cc: > Subject: [CASS SPAM]Re: [gmx-users] How to fix graphite layers? > > If the layers are not identical, use x2top on each layer separately, > combine all layers properly in graphitic stacking order, add topologies нas > needed. If the layers are identical, use x2top only on one, then repeat as > above. > > It is important how the layers are stacked and how they interact, otherwise > the simulation is garbage. > > Alex > > On Tue, Nov 27, 2018, 8:40 PM 高恺 <gaokai...@mails.ucas.ac.cn wrote: > > > Dear all: > > I am currently working on a graphite hole filled with methane. I generate > > my top file by using g_x2top and it works well when there is only one layer > > of graphene. > > But when I use multi-layer graphite, these layers often spread out because > > of insufficient interlayer force. My simulation does not care about the > > mechanical properties of graphite, so I hope that graphite can maintain its > > initial shape. > > > > I have tried position restraints and the top file looks like: > > ------------------------------- > > [ moleculetype ] > > ; Name nrexcl > > GRA 1 > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass > > 1 C2 1 GRA C2 1 0 > > 12.011 > > 2 C2 1 GRA C2 2 0 > > 12.011 > > ……… > > 79586 C2 1 GRA C2 79586 0 > > 12.011 > > > > [ positon_restraints ] > > 1 1 5000 5000 5000 > > > > [ bonds ] > > ; ai aj funct c0 c1 c2 c3 > > 1 5 1 1.420000e-01 5.857600e+05 1.420000e-01 5.857600e+05 > > 1 6 1 1.420000e-01 5.857600e+05 1.420000e-01 5.857600e+05 > > ………… > > > > [ system ] > > GRA+Methane > > > > [ molecules ] > > GRA 1 > > Methane 3500 > > ----------------------------------- > > But it doesn’t seem to work, the graphite molecular layers will still > > spread. > > > > I am also considering freezing a portion of the graphite and keeping the > > graphite in contact with the gas active. Is this feasible? Is there any > > other way to fix the initial shape of the graphite while keeping it at a > > temperature similar to that of a gas? > > > > I would be grateful if anyone could help me. > > > > Kevin Gao > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
