[gmx-users] NPT problem

[Alex]

It is very unclear what you mean by "the results were good" and then "the
results were not good." Your graphene setup is bad and it propagated to
everything else. Please do not start solvating your graphene sample prior
to making sure that your model is reasonable.
To diagnose what's wrong with your model there isn't enough info. For one,
it is unclear if you followed the tutorial correctly. Second, it is unclear
if your x2top command was issued on graphene coordinates with the same box
size as the solvated box, especially if one resulted in proper PBC and the
other did not. Third, you need to turn off all constraints/restraints and
first equilibrate graphene in vacuum (EM followed by considerably long NPT
at something like 10K) and make absolutely sure that PBC is properly set
in-plane, etc, that SP2 bond lengths in graphene are what they are supposed
to be. Fourth, do you understand what that CNT tutorial is doing, or are
you blindly following it?
This stuff requires effort. Noone can help otherwise.

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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