[gmx-users] MD runs wrong!

Diego Enry diego.enry at gmail.com
Wed Nov 2 10:33:22 CET 2005

Is it allways the same atom ? And there are no bad contacts ?
Try to EM with position restraints for protein, them full EM and then CG.

When using
integrator                = cg
I also use
define                      = -DFLEXIBLE   (will take a long time)
constraints              =none

Why don't you give a try to
integrator                  = l-bfgs

Diego Enry.

On 11/2/05, leafyoung81-group at yahoo.com <leafyoung81-group at yahoo.com> wrote:
> --- Samuel Silva Pita <samuelspita at ibest.com.br>
> wrote:
> > Dear GMXers,
> > I'm trying to do a MD run with my protein in water
> > but after EM-through steep and cg- the program runs
> > a MD and give me after some steps a message: "atom
> > 108708 can not be settled. Check for bad contacts
> > and/or reduce the timestep. I tried to do this but
> > the problem persist.
> Have you used position-restrained MD for equilibration
> before MD?
> Yang Ye
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Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.

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