Dear Amber users,
I am trying to run nmode on a protein with 320 residues, and nmode seems
to run out of memory.
here is the input file:
Lipase vibrational analysis
&data
ntrun=1,
scee=1.2,
cut=12.0,
nvect=482,
idiel=0,
ivform=0,
ilevel=0,
drms=100
&end
and the output:
0 1 5210 10420 15630
15887 16400 16915 19787 22659
25531 27916 30301 32686 37845
43004 48163 53322 56590 59858
63126 66394 81967 97540 113113
128686 144259 159832 175405 190978
206551 222124 248368 253577 269206
279626 284836 53012 68639 99893
295256 122214481 300466 122214481 122355124
122370751 0 0 0 258786
263996 47803 0
Total memory required : 129902965 real words
Total memory avail : 3500000 real words
Total memory required : 300466 integer words
Total memory avail : 4000000 integer words
Maximum nonbond pairs 3699533
increase the real memory by 126402965 words
-----
i am trying to run this on a Linux box with 64M memory and 130M virtual
Is there a way to estimate how much is required?
(what is the size of a real word?)
i am also wondering about the available memory it reported, it seems very
low...
Thaks,
Gusztav Schay.
ps.: many thanks for the answeres on my problem with sander ewald stuff,
it really was the config of the periodic box..
-----------------------
Gusztav SCHAY
PhD student
Semmelweis University Budapest
Dept. of Biophysics and Radiation Biology
Budapest
Puskin u. 9.
H-1088
Hungary
phone: +36-1-2662755 #4033
fax: +36-1-2666656
email: schayg_at_puskin-a206.sote.hu
-----------------------
Received on Thu Sep 28 2000 - 05:35:46 PDT
