Hi Yanmei, I had this problem with water molecules, and I found that any time I changed the constrains without changing the boxes I generated through 'editconf'. So, after changing the constrains, I had to redo all my box generation process, then it was fine. But I ran into another problem and that was I had a separate row of molecules out of my box (which I do not know where they come from)!
Payman From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: May 7, 2009 6:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] Some molecules disconnected into many parts after EM 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! -- Yanmei Song Department of Chemical Engineering ASU
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