spss4 at iacs.res.in spss4 at iacs.res.in
Fri Jun 7 07:28:12 CEST 2019

I think this is due to the periodic boundary condition. Once you try  
to cut the .gro file using -pbc mol by gmx trjconv command. Hope this  
will work otherwise it is your system error, you need to modify your  
molecule topology file.
----- Message from Dhrubajyoti Maji <dmaji43 at gmail.com> ---------
    Date: Thu, 6 Jun 2019 11:23:36 +0530
    From: Dhrubajyoti Maji <dmaji43 at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: [gmx-users] ENERGY MINIMISATION
      To: gromacs.org_gmx-users at maillist.sys.kth.se

> Dear gromacs family members,
>         I am doing energy minimisation of a 250 molecule  acetamide system
> in gromacs 2018.3. The energy minimisation process runs smoothly without
> any warning. But when I see the resultant gro file through VMD I find
> several bonds are broken. Please suggest about this problem.
> Thanks
> Dhrubajyoti Maji
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----- End message from Dhrubajyoti Maji <dmaji43 at gmail.com> -----

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