MD problem

From: bo baker (
Date: Sun Mar 26 2006 - 16:54:38 CST

Hello, NAMD:

I submitted the protein-membrane-water system to NAMD for a production
run. I has been running fine, until reach to 53200 timestep. The run
just stops there, and does not go further. Here is details of the last
step from the .log file:

TIMING: 532000 CPU: 1.41196e+06, 3.89498/step Wall: 1.41255e+06,
4.00398/step, 142.364 hours remaining, 0 kB of memory in use.
ENERGY: 532000 14506.3683 16443.6729 4714.3435
144.7458 -130123.1078 5814.1059 0.0000
0.0000 42588.2680 -45911.6035 306.9037
-45371.9327 -45361.8119 308.3844 1289.8041
-145.7511 449606.5801 -38.0757 -38.0907

I then submitted another short run. It works fine, indicating the
computer system is OK. But my MD run just stop there without generate
the .coor , .vel and .xsc files. I can manage to create the .coor file
from the .dcd, and .xsc file from the .xst, but don't know where can I
find the information about the last .vel file. Without this file, I
can't start anohter run from where it stoped. Can any one give me
suggestion on how to rescure the frozen run? And is there a way to set
the freq to save .vel file from the .conf file?

I use NMAD 2.6b1, and run it in a Mac OSX 10.3. The computer has
running spaces.

Thank you.



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