Dallas Warren dallas.warren at monash.edu
Thu Jun 6 08:43:11 CEST 2019

.gro files do not contain any information about bonds, only the coordinate
of each atom/particle. VMD guesses which atoms are bonded together based on
their separation.

On Thu, 6 Jun. 2019, 3:53 pm Dhrubajyoti Maji, <dmaji43 at gmail.com> wrote:

> 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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