[gmx-users] about mdrun errors!! again

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Feb 18 14:34:36 CET 2003


If you allowed a suggestion, check for overlaping rings.  I mean, once,
generating structures I created overlaping rings, forming chains, and
energies goes to space.  Days wasted until I founded it.

VMD can show you bump atoms.  And, as Dr. Spoel said, check EM output.

On 18 Feb 2003, David van der Spoel wrote:

> On Tue, 2003-02-18 at 09:29, nanyu101 wrote: > Dear Dr.David, > Thanks
> for your prompt reply.If my puzzle as you told that the large force
> was caused by the atoms being too close in the starting
> conformation.How can I fix it?I have already run EM and optimize it. >
> You have to find out what is causing the large forces. em tells you
> which atom has the highest force. Genbox does not generate
> conformations with overlapping atoms. Maybe you check the make hole
> program from Graham Smith. (on gromacs website)

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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