RE: namd-1: Simulation Terminating Early

From: Norman Geist (
Date: Mon Feb 09 2015 - 03:09:57 CST



we will likely need to see your namd input. You are using Windows right? What NAMD binary do you use?


Actually your simulation seem to become unstable:


For now there are several options to try:


1. increase minimization steps

2. set dcdfreq to a low number, maybe 1 and check the behavior of the simulation visually for instability

3. run on a different machine to exclude problems with your hardware


Norman Geist.


From: [] On Behalf Of Akshata Rudrapatna
Sent: Saturday, February 07, 2015 10:07 PM
Subject: namd-l: namd-1: Simulation Terminating Early


Hello NAMD Community,


I posted earlier about not being able to run the example simulation given in the NAMD tutorial on the website. I was able to get the simulation started and running, but it runs approximately one minute before terminating.


The last message in the log is as follows:



TCL: Running for 100 steps

PRESSURE: 100 -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND

GPRESSURE: 100 -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND -1.#IND

ENERGY: 100 91.8776 243.3225 250.4144 8.5143 -14084.3172 1235.7567 0.0000 0.0000 -1.#IND -1.#IND -1.#IND -12254.4316 -1.#IND -1.#IND -1.#IND -1.#IND 86856.0000 -1.#IND -1.#IND


I have tried changing the timestep and the pairlistdist values in the file, as well as the length of time the simulation runs for.


Does anyone have any suggestions or tips as to how to resolve this problem?

I appreciate your time and consideration.




Akshata Rudrapatna

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