AMBER Archive (2008)

Subject: RE: AMBER: mwcovar limit?

From: Ross Walker (
Date: Wed Dec 31 2008 - 22:44:33 CST

Hi Claudio,


I have not tried mwcovar however I would suggest that you check a couple of
things - the main ones related to having a 64 bit OS and 64 bit compilation.
Firstly if you are on a EM64T machine make sure you have the 64 bit version
of the OS installed. Next make sure you are using the 64 bit version of the
compiler (no -m32 / -tpp p7 options etc) and make sure it is compiling a 64
bit executable and linking to the 64 bit libraries.


Finally make sure your stack and datasize limits are all unlimited - see the
"limit" or "ulimit" command. Note there may be system wide limits that mean
you need to be root to set values greater than 4GB.


Good luck,




From: [] On Behalf Of
Carra, Claudio (JSC-SK)[USRA]
Sent: Monday, December 29, 2008 2:31 PM
Subject: AMBER: mwcovar limit?


Dear All,

I was trying to test mwcovar as initial step to perform

a quasiharmonic analysis, with amber10.

Unfortunately I got a segmentation fault

when I consider more than ~10917 atoms, 722 residues, ~4Gb RAM.

Iíve no limit in RAM use and the memory available is more than 10Gb,

so technically it should work for more atoms.

My question is if there are any limit in the size of the system analyzed

with mwcovar.

thanks a lot





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