AMBER Archive (2008)

Subject: AMBER: nmode: number of atoms limitation

From: Qi Yan (
Date: Wed May 07 2008 - 13:10:48 CDT


I'm using amber9 to do nmode analysis. The atoms in my system are 8454
which are more than maxatom=8000 written in sizes2.h.

Therefore I did some modification as below
parameter (memdrv=10000000)
parameter (maxatom=9000)
parameter (maxint=500)
parameter (maxvec=500)
parameter (maxdih = 55000)
parameter (maxdia = 35000)
parameter (maxinb = 90000)
parameter (maxbon = 26000)
parameter (maxbnh = 20000)
parameter (maxang = 30000)
parameter (maxanh = 30000)

and then I recompiled nmode. Actually, nmode can work after this
modification, but when I check the process of CPU, I found that %CPU is
~4 which is too small and %MEM is ~90 which is very high. The nmode with
8454 atoms has been running for a whole day and I still can not get
result. When I use a system with 3244 atoms to test this recompiled
system, it worked very well and I can get the result within 20 minutes.

Does anybody know what is the reason?

Thanks in advance,


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to