[gmx-users] NPT problem
Mohammad Roostaie
mohammad.r0325 at yahoo.com
Fri Jul 14 09:12:17 CEST 2017
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?
Thanks,Mohammad
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>;
> Mohammad Roostaie <mohammad.r0325 at yahoo.com>
> *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.
>
>
> 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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