AMBER Archive (2008)

Subject: AMBER: nmode: number of atoms limitation

From: Qi Yan (kid1412_at_uab.edu)
Date: Wed May 07 2008 - 13:10:48 CDT

Hi,all:

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,

Qi

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu