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
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