AMBER Archive (2008)

Subject: Re: AMBER: Nmode segmentation fault

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 02 2008 - 12:50:09 CDT

On Tue, Mar 25, 2008, James Thomas wrote:

> The input file:
> &data
> ntrun=4,
> nsave=2,
> ndiag=2,
> cut=95.0,
> nprint=100,
> drms=0.00001,
> maxcyc=100,
> bdwnhl=0.01,
> dfpred=0.1,
> scnb=2.0,
> scee=2.0,
> nvect=200,
> ntxo=1,
> &end
>
> The machine:
> I run it on Opteron-based compute cluster, it has a head node with dual
> Opteron 246 CPUs, 4GB RAM and mirrored 160GB SATA disks.
> The OS is SuSE Linux 9.3

Sorry to be slow in replying. Two notes:

1. nmode is being retired, and equivalent NR minimization (better, actually,
since it supports GB as well as gas-phase force fields) is available in NAB.
See:
         http://ambermd.org/#AmberTools

However, there is admittedly a learning curve here, so we would also like to
fix nmode if we can reproduce the problem.

2. So, can you send the prmtop and inpcrd files you are using? Until we
can reproduce the problem, it is unlikely to be fixed.

...regards...dac

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