From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Feb 24 2004 - 15:31:06 CST
Hi,
There is no compiled-in limit for NAMD, although one struct definition
limits the atom id to 22 bits, or just over 4 million atoms. Growing
pains start at around 1 million atoms from what I've seen, assuming you
have enough CPUs and disk space to work with such a beast.
Your system is quite typical. While the atomid field in a pdb file is
only five characters wide, it contains no real information and NAMD
ignores any bogus values when that field overflows, as happens with
systems of 100,000 atoms.
-Jim
On Wed, 18 Feb 2004, Wei Fu wrote:
> Hi,
>
> After adding water, my system has 121874 atoms. How many atoms does NAMD can run?
>
> Fu, Wei
>
> 2004-02-18
> ************************************************************
> Wei Fu (Linda)
> Postdoctoral Research Associate
> Department of Biology and Biochemistry
> University of Houston
> 4800 Calhoun Rd. HSC #402C
> Houston, TX 77204-5001 USA
> Phone:713-743-8355(o) 713-795-9270(h)
> Fax:713-743-8351
> Email: fuwei_at_adrik.bchs.uh.edu
> http://adrik.bchs.uh.edu/~fuwei/
> **************************************************************
>
>
>
>
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