[gmx-users] Fragmentation of molecule during final md

[Mark Abraham]

On 26/07/2012 4:47 PM, radhika jaswal wrote:
> Hi all,
>
> I ran a simulation of a molecule in box. The molecule was intact during the position restraint step, bit after the final md of 1 ns it broke down into 2 parts. I am using the GroMACS version 4.5.4 and Berendsen thermostat with ref_t = 300 K. What could be the reasons for this fragmentation?
>
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark