[gmx-users] pull code for speptide

[ysun at mie.utoronto.ca]

Thanks to Marc,

I am not sure if Gromacs could stretch on a group of molecules?
  
I WOULD appreciate if you could advise me more detail and suggest how to modify 
my pull code.

Thanks again.

Sun  


Quoting Marco Ceruso <mceruso at physbio.mssm.edu>:

> 
> Hi,
> AFAIK the pull code is not meant to "stretch" a molecule but to pull a
> molecule/ion away/towards another molecule
> Marc
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of ysun at mie.utoronto.ca
> Sent: Monday, August 11, 2003 12:44 PM
> To: gmx-users at gromacs.org
> Cc: ysun at mie.utoronto.ca
> Subject: Re: [gmx-users] pull code for speptide
> 
> 
> Dear GMX-users,
> 
>  Since no reply to my previous question, I want to seek your help again.
> 
>  I am trying a pull code on example: speptide (under tutor/speptide).
>  I applied pulling on a top atom (atom 9) and freeze at a bottom atom (atom
>  140),
> 
>  and used
> 
>  grompp -f pr.mdp -o prpull3 -c after_em -p speptide -n index.ndx
> 
>  mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g
> prpull3.log
>  -
>  pi pull.ppa -pn index.ndx
> 
>  The error came out:  "floating exception"
> 
>  Would appreciate if you could help me to identify the problem.
> 
>  I attached relevant files here for your information.
> 
>  Thanks in advance!
> 
>  Sun
> 
> 
> 
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