[gmx-users] Fragmentation of molecule during final md

radhika jaswal jaswalradhika at yahoo.co.in
Thu Jul 26 08:47:15 CEST 2012

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.

Panjab University,
Chandigarh, India.

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