Subject: Normal Modes for large proteins

From: Ben Carrington <[email-masked]>
Date: Tue, 26 Feb 2002 19:21:22 +0000 (GMT)

Dear all,

Can anyone suggest how I go about performing normal modes calculations
on large systems - protein complexes to be exact. At the moment I cannot
get any programs to run due to the large amount of memory needed. Can I
split this calculation up?

Yours hopefully,

Ben

[email-masked]

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From: Szilveszter Juhos <[email-masked]>
Date: Tue, 26 Feb 2002 21:09:33 +0000 (GMT)

> split this calculation up?

As a novice in MD I can say that likely not :( But why are you running out
of memory? Is it beacuse you do not have enough physical memory (that
should not be a problem novadays) or because your user resource is limited
(check the 'limit' command using tcsh or 'ulimit -a' with bash)?  If you
give more details about the error you get...

Szilva