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

Payman Pirzadeh ppirzade at ucalgary.ca
Fri May 8 02:15:26 CEST 2009

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)!




From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Yanmei Song
Sent: May 7, 2009 6:06 PM
To: gmx-users at 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

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