Re: MD problem

From: Peter Freddolino (
Date: Sun Mar 26 2006 - 18:19:13 CST

Dear Bo,
in general, you can set the rate at which restart files are written with
the "restartfreq" keyword. In your case, are you saying you had no
restart files after 53200 timesteps? Did you set "restartname"? Please
for more on how to set up restart files.
Also, did your namd run crash or hang? Is there still a namd process
left over after this happened?

bo baker wrote

>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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