From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Tue Aug 18 2009 - 03:23:20 CDT
I am doing a simulation (restart) taking the coordintes from the previously
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
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..
Gurunath M Katagi
Supercomputer Education and Research Center
Indian Institute Of Science
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