Re: restating simuation and periodic cell conditions

From: Chris Harrison (
Date: Tue Aug 18 2009 - 07:08:07 CDT

Try adding "margin 5" for a few 100 picoseconds to nanosecond in a restart,
then removing it in the subsequent restart.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Tue, Aug 18, 2009 at 3:23 AM, gurunath katagi <>wrote:
> Dear all,
> I am doing a simulation (restart) taking the coordintes from the previously
> minimized sytem...
> However, i got the following error,
> TCL: Suspending until startup complete.
> Info: EXTENDED SYSTEM FILE   ../output1/hemo_wb.restart.xsc
> FATAL ERROR: PME requires periodic boundary conditions.
> but, in the namd-tutorial on ubqiquitin, it mentions us to not to give the
> periodic conditions when restarting the simulation.
> i have attatched the config file: protein.conf
> Next, if i do not include the periodic conditions as per the tutorial
> ,(just comment out the periodic conditions part), i am getting the
> folllowing error..
> ERROR: Margin is too small for 366 atoms during timestep 5501.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> can anybody look into this and suggest me possible solutions..
> Thank you
> Gurunath M Katagi
> Graduate Student
> Supercomputer Education and Research Center
> Indian Institute Of Science
> Bangalore

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