Dear Justin: Thanks for your message.
When I open the gro file using VMD it shows: atom:1950 bonds 1907 residue:43 I was thinking the problem may not come from the artifact of visualization. Since if the gro file is fine it should be like: atom:1950 bonds 1944 residue:6 because I have 6 chains in the box. This morning I found that it seems the problem was resolved by increasing the box size. Why is that? On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Yanmei Song wrote: > >> Dear users: >> >> I set up a 8nm cubic box with 6 long chain molecules. After EM, there is >> no error message. However I found that in the gro file by visualization, 2 >> of the chains has been split in many parts, which means many bonds in the >> molecules disconnected. And also the other 4 are good. I checked em.log and >> eveyting looks fine. >> >> Steepest Descents converged to machine precision in 1545 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.51461594735782e+03 >> Maximum force = 2.66505909651672e+02 on atom 1256 >> Norm of force = 9.84300153087768e+00 >> >> Anyone knows how to solve the problem? Thanks in advance! >> >> > Probably an artifact of visualization, or otherwise periodic boundary > conditions: > > http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions > > -Justin > > -- >> Yanmei Song >> Department of Chemical Engineering >> ASU >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU
_______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php