[gmx-users] Microporous simulation

[Hernan Ahumada]

 Hi everyone

I am trying to run a simulation of Alpo (aluminophosphates) microporous
material,  the topology of the material was build using x2top (it had been
checked).  I got all the bonding and nonbonding parameters, when I run the
energy minimization of this system, Iget this :

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        10000
There were 420 inconsistent shifts. Check your topology
Step=    0, Dmax= 1.0e-02 nm, Epot=  3.25885e+04 Fmax= 0.00000e+00, atom= 0

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 10 in 1 steps
Potential Energy  =  3.2588531e+04
Maximum force     =  0.0000000e+00 on atom 0
Norm of force     =  0.0000000e+00

gcq#152: "I Smell Smoke From a Gun Named Extinction" (Pixies)

When I look my finally PDB the structure of microporus material,  some atoms
appear outside the box. I don't know how to fix the atoms inside the box? and
avoid this inconsistent shift. who can help me with this?

Thanks

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