[gmx-users] Error while running methane in water simulation

vivek sharma viveksharma.iitb at gmail.com
Thu Oct 13 08:30:49 CEST 2011

Hi there,
I am trying to run the free energy tutorial by David mobley mentioned at *h
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
Thanks and regards,
*Vivek Sharma*
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