[gmx-users] How to make the broken molecule into one

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jul 27 07:38:30 CEST 2012

On 27/07/2012 2:08 PM, radhika jaswal wrote:
> Hi,
> Just read, http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. But could not get it.
> Please suggest hoe to fix the visual issues with the molecule being broken into two parts in the final simulation.

There's a suggested workflow on that page. There is no magic way to make 
things look how you want that works in all cases, so mdrun makes no 
attempt. So thinking and reading and experimenting based on that 
workflow are needed.


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