[gmx-users] ENERGY MINIMISATION

[Dhrubajyoti Maji]

Hi,
   Many thanks for your reply. I have used gmx trjconv with -pbc mol and
now the system looks fine.
   Thanks again. Regards
   Dhrubajyoti

On Fri, 7 Jun 2019 at 10:58, <spss4 at iacs.res.in> wrote:

>   Hii
> 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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