AMBER: more than 100,000 atoms ?

From: David Smith <>
Date: 07 Aug 2003 21:44:23 +0200

Hi all,

Apologies if this question has come up before but I don't remember it
and a quick search of the archives didn't net me anything.

I wanted to try a system with more than 100,000 atoms. I know it's a bit
big but my boss is an ambitious guy.....

I gave it a go and initially got very confused by getting caught by
"Peek Ewald" in a simple sander minimization.

After a bit of surprise and a few write statements I realized that NATOM
was being read as "I5" from the CRD file. Changing it to "I6" got me
past "Peek Ewald" but I then got stuck a bit later. The web page tells
me that, in general, NATOM is "I6" in PARMTOP but "I5" in CRD.

I am still "trapped" in Amber 6 but my guess is that these formats
persist into Amber 7 ?

Can anyone recommend a way to do such a system with AMBER (any version)?

i.e. Would I have to change all the formats associated with "read (9,F)"
statements. Is there a semi fast way to do it ? Even if I did manage
that, would the developers imagine that something else would break and
that I should simply abandon the whole idea.

Thanks for your patience ....


Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
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Received on Thu Aug 07 2003 - 20:53:00 PDT
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