Hi there, I am trying to run the free energy tutorial by David mobley mentioned at *h ttp:// www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial* While running a test run for lambda value of 0, I found that there is some problem with the generated trajectory, I observed the distorted (straight lines running between box edges) methane structure in the water box while viewing the co-ordinate movie. Thinking that, this scenario relates to the periodic boundary conditions. I checked the parameter file where *pbc = xyz.
*Please suggest what may be the reason for the distortion in methane during simulation.* * Thanks and regards, *Vivek Sharma*
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