From: Chris Harrison (charris5_at_gmail.com)
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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Tue, Aug 18, 2009 at 3:23 AM, gurunath katagi <gurukatagi_at_gmail.com>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.. > OPENING EXTENDED SYSTEM TRAJECTORY FILE > 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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