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:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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