# [gmx-users] NPT problem

Alex nedomacho at gmail.com
Fri Jul 14 22:28:15 CEST 2017

```No, I mean that:

1. Graphene dimensions cannot be exactly 9 x 9. It is a crystal and its
in-plane dimensions are _precisely_ determined by the unit cell counts in
the corresponding directions.
2. The box size needs to be adjusted in accordance with basic geometry of
the crystal and its lattice orientation relative to the rectangular box.
3. With a difference of 2 nm between box size and sample dimensions, there
is no way your PBC  request is properly processed by x2top. You are likely
obtaining a finite sheet instead of a self-passivated periodic sheet and
then edges are causing issues.
4. Until you make some effort to learn about graphene and crystals (prior
to solvating and doing other things), nothing will work and noone here will
be able to help.

Alex

On Fri, Jul 14, 2017 at 1:09 AM, <mohammad.r0325 at yahoo.com> wrote:

> The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean
> that the box dimensions are small and thats the problem?
>       From: Alex <nedomacho at gmail.com>
>  To: Discussion list for GROMACS users <gmx-users at gromacs.org>;
> Discussion list for GROMACS users <gmx-users at gromacs.org>
>  Sent: Friday, 14 July 2017, 11:31:06
>  Subject: Re: [gmx-users] NPT problem
>
>
> >
> > I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT
> > -noparam -pbc" for generating the topology. then I used "gmx editconf
> > -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating
> > the box
> >
> And where did "-box 11 11 11" come from? For pbc to work the box in your
> case has to be a certain size corresponding to the graphene dimensions.
> And no, it is not simply its approximate X-Y dimensions.
>
> Alex
>
> >
> > ------------------------------------------------------------------------
> > *From:* Alex <nedomacho at gmail.com>
> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>;
> > *Sent:* Thursday, 13 July 2017, 22:51:48
> > *Subject:* Re: [gmx-users] NPT problem
> >
> > 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
> > <mailto: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
> >    <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.
> >
> >
> >    the position restrain on the graphene. I really would appreciate
> >    any help.
> >
> >
> >    If you need further information please let me know.
> >
> >
> >
> >    --
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> >
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> >
> >
>
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