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
