[gmx-users] Microporous simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 20 15:39:23 CEST 2011

Hernan Ahumada wrote:
>  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?

The inconsistent shifts and high potential energy indicate that the system has 
blown up due to instability.  There is no way to simply "fix" the atoms in the 
box aside from preparing a system that can actually be energy-minimized.

It is odd to me that the force is zero.  Which Gromacs version is this?  What 
hardware are you running it on, and how did you install it (exact commands, 
please)?  I ran into this problem a long time ago due to an as-yet unresolved 
bug, but I am hesitant to suggest that without knowing a whole lot more about 
your setup.


> Thanks
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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