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

[vivek sharma]

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*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111013/02dee1c2/attachment.html>