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.
-Justin
Thanks
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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