AMBER Archive (2004)

Subject: AMBER: memory problem in NMODE

From: xhu1_at_memphis.edu
Date: Mon Apr 19 2004 - 15:06:46 CDT

Dear All,

I am doing normal mode analysis of protein by nmode of amber 7. The
protein has 198 residues(1520 atoms). I got a memory problem:

>Total memory required : 132758715 real words
>Total memory avail : 15000000 real words
>Total memory required : 202865 integer words
>Total memory avail : 4000000 integer words

>Maximum nonbond pairs 3797134
>increase the real memory by 117758715 words

I increased the real memory to 140000000 at sizes.h file, and tried
again. This time I got "Segmentation fault...(core dumped)". Is my
physical memory too small? Currently there are 2G memory in my
workstation. If it is, then how much memory I should use in my
calculations? Any suggestions will be highly appreciated! Thank you so
much!

Best

Shawn Hu

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