[gmx-users] pull code for speptide

Marco Ceruso mceruso at physbio.mssm.edu
Mon Aug 11 18:59:01 CEST 2003

AFAIK the pull code is not meant to "stretch" a molecule but to pull a
molecule/ion away/towards another molecule

-----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

 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
 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!


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