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

[Justin A. Lemkul]

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
> 
> 
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-- 
========================================

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

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