AMBER: nmode ntrun=2

From: JM Beames <>
Date: Wed, 05 Dec 2007 10:03:24 +0000

Hi everyone,

I am trying to run a transition state search using nmode in amber9. The
molecule that I'm currently using runs happily in ntrun=1 and ntrun=4 but
whenever I try and use ntrun=2 I get a segmentation fault. I have tried
this with varying flags in the nmdin file, including using solely ntrun=2
to allow all other values to default, but also setting almost all the
variables, including changing the files between formatted and unformatted,
and increasing the drms value. None of these things seem to alter the
result I get which is that generally the first step (ie. step=0) is written
to the .out file and then I receive the segmentation fault error. I have
attempted to run this in debug mode, but unfortunately can make no sense of
the output. The molecule I am using is not large (78 atoms with no metals)
and so computationally I think this should be achievable. Could someone
help me out if there are any special flags I should be using here or if
there is a useful tutorial on ntrun=2 section of nmode as I am yet to find
one. I'm afraid I can't give specifics on the error as the only error
message saved is Segmentation Fault.

Many thanks in advance

Joe Beames

JM Beames
Laser Group
Department of Chemistry
University of Bristol
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Received on Sun Dec 09 2007 - 06:07:05 PST
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