about restart

From: namd_chcwaaa_at_yahoo.com.cn
Date: Thu Oct 08 2009 - 06:46:07 CDT

Dear NAMD users,
    After 10000 steps run, I restart the simulation (for 80000 steps) using coor, vel and xsc files generated at the last step (10000). At the beginning of the restart run, NAMD calculates and outputs some parameters at step 10000. There are small differences of energy values at step 10000 between the first and the restart run. I think the reason is the loss of accuracy because the coor, vel and xsc files were generated using nonbinary mode. However, the pressure values are quite different. So, I am wondering is the pressure calculated using different schemes after restart?
    In the 80000 steps restart run, NAMD quits at step 40000 because of the error that some atoms move too fast. But, when I restart the simulation from step 39500 (the restart files are generated every 500 steps), it goes well without further errors that some atoms move too fast. I don't know why?

    The questions may be quite simple for some of you. Please do not hesitate to give me some advice. I would be greatly appreciate for any suggestions. Thank you for reading.

2009-10-08

cong chen

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