[gmx-users] Fragmentation of molecule during final md

[radhika jaswal]

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?

Thanks in advance.

Radhika,
Panjab University,
Chandigarh, India.