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 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
