AMBER Archive (2008)

Subject: Re: AMBER: Error runing Addles

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 22 2008 - 07:48:07 CDT

is this from multiple tests? I'm not clear what is in the input vs
what the result is.
what is the "pack=2" for?
what does the addles.out file have?
do the LES tests pass?

On Thu, Aug 21, 2008 at 11:25 PM, Shultz, Jack <JShultz_at_nas.edu> wrote:
> I get these error message running addles. Is my molecule too big? I have
> 1973 atoms.
>
> file rprm name=(str1.prmtop) read
> file rcrd name=(str1.inpcrd) pack=2 read
> file wprm name=(neb.prmtop) wovr
> file wcrd name=(neb.inpcrd) wovr
> action
> ~ use original mass
> omas
> pimd
> ~ make 1 copies of atom 1 to 1973 (the whole system)
> space numc=1 pick #prt 1 1973 done
> *EOD
>
> $ $AMBERHOME/exe/addles <addles.in >addles.out
> 21 [main] addles 3656 _cygtls::handle_exceptions: Error while dumping
> state
> (probably corrupted stack)
> Segmentation fault (core dumped)
>
> space numc=2 pick #prt 1 1973 done
> $ $AMBERHOME/exe/addles <addles.in >addles.out
> 630 [main] addles 2676 _cygtls::handle_exceptions: Error while dumping
> state
> (probably corrupted stack)
> Segmentation fault (core dumped)
>
> ~ make 2 copies of atom 1 to 3 (the whole system)
> space numc=2 pick #prt 1 3 done
>
> $ $AMBERHOME/exe/addles <addles.in >addles.out
> 22 [main] addles 3864 _cygtls::handle_exceptions: Error while dumping
> state
> (probably corrupted stack)
> Segmentation fault (core dumped) 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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