[gmx-users] NPT problem

[Alex]

Also, that tutorial's parameters that are completely wrong for graphene.
For bulk graphene bond types I suggest:

  CJ    CJ      1    0.14200   420420.0

For bulk angles:

  CJ     CJ     CJ      1   120.000    659.346

For bulk dihedrals:

  CJ     CJ     CJ     CJ      3     17.30770   0.00000 -17.30770   0.00000
  0.00000   0.00000

These are parameters obtained from a Taylor-expanded optimized
Tersoff-Brenner potential. Please count the number of bonds and dihedrals
in your graphene model, as produced by x2top. If the number of dihedrals
divided by the number of bonds gives you a number, say, equal to m, then
multiply the dihedral parameters by that number. And do NOT use bond
constraints -- you are simulating a crystal.

Alex

On Thu, Jul 13, 2017 at 10:45 AM, <mohammad.r0325 at yahoo.com> wrote:

> Hi All GROMACS users,
>
>
>
> I created graphene with nanotube modeler then I created a force field for
> graphene based on OPLS (by using this link and its parameters:
> http://chembytes.wikidot.com/grocnt). I generated the topology file using
> x2top command. I put the graphene inside a box of water (TIP3P) which was
> larger than the graphene dimension with 1000  (kJ/mol nm^2) position
> restraint on all the atoms, and I performed the energy minimization and NVT
> equilibrations (in order to get an optimized structure of the graphene for
> further simulations). The results of both of them were good (energy level
> has reached a negative value with the order of 6 and the temperature has
> converged the preferred value). But, when I run the NPT equilibration, the
> results are not good (the pressure and density fluctuated very much and the
> averaged values are so far from the preferred ones). Also, during the NPT
> run, I received these messages:
>
>
> step 53965: Water molecule starting at atom 127424 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 141454: Water molecule starting at atom 53366 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 141483: Water molecule starting at atom 53366 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323815: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323816: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323818: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355712: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355714: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355716: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355718: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469414: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469416: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469418: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469420: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> , and a pdb file was saved after each step.
> In addition, something interesting is that I performed another run with
> all of the previous parameters, except I did not put position restraint on
> the graphene, and the results of NPT were good and acceptable, and I did
> not get those messages.
>
>
> Can you please help me figure this problem out? Since I should put the
> position restrain on the graphene. I really would appreciate any help.
>
>
> If you need further information please let me know.
> Kind regards,Mohammad
>
>
>
> --
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