restating simuation and periodic cell conditions

From: gurunath katagi (
Date: Tue Aug 18 2009 - 03:23:20 CDT

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: 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

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