AMBER: nmode calculation

From: mingche Pan <>
Date: Fri, 21 Jan 2005 17:43:32 -0800 (PST)

Dear all,


I¡¯d like to do some nmode calculations. My system is rather big, having 6660 atoms (need ~1.7 G memory with amber6, and ~3.2G memory with amber8). I have tried different ways on different machines to test nmode compilation and execution, but no luck. I summarized the testing results as below.



On Dell PowerEdge 1750, 3.2G dual Intel Xeon (32 bits system), 4G memory

(Note: with Hyper-Threading on)




   MAXMEMX= 110,000,000

Compilation: OK

Execution: OK for small system


   MAXMEMX= 120,000,000 ¨C 260,000,000

Compilation: OK

Execution: Segment fault, core dumped by only typing ¡°nmode¡± command


   MAXMEMX= 270,000,000 ¨C

Compilation: unsucceeded, ¡°x¡± is too large to handle, ¡°store_x_¡± is too large.

Execution: -




MEMDRV = 400,000,000, MAXATOM = 7000, etc.

Compilation: OK

Execution: failed due to insufficient memory (ASSERTion 'ier == 0' failed in nmode.f at line 105.)



On SGI, 64bit, 64G memory


Amber6: MAXMEMX= 500,000,000

Compilation: using ¡°-64¡± instead of ¡°-n32¡±, succeeded!

Execution: works for small system, but core dumped after running my job, but no Segment fault error by typing ¡°nmode¡± command


Amber8: MEMDRV = 400,000,000, MAXATOM = 7000

Compilation: using ¡°-64¡± instead of ¡°-n32¡±, OK

Execution: works for small system; core dumped again for my system!!!! Different error message, it says memory available is only 260,000,000 (2G), asking to increase the memory!!!




My questions are:

   Can I get nmode (version 6) to work with my system on Dell machine?


   What is the problem with nmode calculation on SGI machine? (on both machines, I have no limitation of disk and memory usage)


Can anyone give me a hand? Sorry for the lengthy message and thanks for any suggestion!!





Do you Yahoo!?
 Yahoo! Mail - Easier than ever with enhanced search. Learn more.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sat Jan 22 2005 - 01:53:00 PST
Custom Search