[gmx-users] Some molecules disconnected into many parts after EM

Yanmei Song ysong30 at asu.edu
Fri May 8 02:05:37 CEST 2009

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
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