It seems because your box should be a bit longer to succeed. Try to enlarge the side (13.2 nm) length.
2008/8/21 Andy Shelley <[EMAIL PROTECTED]>: > No problem the term flattens is porbably not the best technical > description. A better one would be the cnt collapses. > > Andy > > On Thu, Aug 21, 2008 at 8:34 AM, Vitaly Chaban <[EMAIL PROTECTED]> > wrote: >> >> > >> > Actually I think I am using the gromos force field. I have been using >> > Christopher Stiles page as a guide to get started with using CNT >> > http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications >> > were >> > made to ffgmx files. So I believe I am using the gromos forcefield. Is >> > the >> > forcefield used defined by the parameters? I have added nonbonded >> > parameters >> > to ffgmxnb.itp as the following: >> > [ nonboned_params ] >> > O N 1 0.0069 1.4016E-05 >> > O O 1 0.0061 9.9676E-06 >> > N N 1 0.0076 1.8778E-05 >> > C O 1 0.0030 4.7908E-06 >> > C N 1 0.0033 6.5271E-06 >> > >> > and the same for pairtypes >> > [ pairtypes ] >> > C N 1 0.0033 6.5271E-06 >> > C O 1 0.0030 4.7908E-06 >> > N N 1 0.0076 1.8778E-05 >> > O O 1 0.0061 9.9676E-06 >> > O N 1 0.0069 1.4016E-05 >> > >> > I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box >> > with a 10,10 cnt length 12.3nm. The nitrogen molecules appear to not >> > even >> > interact with the cnt but it still flattens. Any ideas? >> > >> >> Andy, >> >> Hi. Sorry for my English, what do you mean saying "cnt flattens"? >> >> Again, is everything right with your box side length. I mean if the >> cnt fits in the box (the rim atoms)? >> >> >> -- >> Vitaly V. Chaban >> School of Chemistry >> National University of Kharkiv >> Svoboda sq., 4, Kharkiv 61077, Ukraine >> email: [EMAIL PROTECTED] >> skype: vvchaban > > -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban _______________________________________________ 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
