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

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 13 12:52:22 CEST 2011

vivek sharma wrote:
> 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 
> <http://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.*
> *

This outcome is the expected result of PBC.  You need to post-process the 
trajectory to account for this behavior.  See the workflow here:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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