[gmx-users] help on Graphene Nano Sheets
Marcello Cammarata
marcello.cammarata at unipa.it
Wed Apr 29 19:07:04 CEST 2015
I am still in trouble with Graphene layers.
I study come aspects about bond, dihedral and improper dihedral from
blog and manuals.
My layer of grafene, and my nanotube still go to collapse, during a em
simulation.
I did not find nothing about the all_dihedral parameter in bondedtype,
in rpt file, I try to copy my force field set suggested from Minoia in
all itp files: forcefield ffbonded and ffnonbonded,
i try to change parameters in dihedrals from 1 to 3, and in RemoveDih
from 0 to 1. I try to add periodic_molecules=yes in mdp file, but i am
still away from my goal.
Sorry Alex, you said that i don't have to change the dihedrals from 1 to
3 in the top file, but with if i don't change it i always get the
error: No default Proper Dih. types, for all 168 dihedrals,
also you suggest to add something in ffbonded.itp but i don't know what.
An other thing that i want to try is to block one side of the graphene
layer, i was surfing on line and i find this:
[ moleculetype]
This_one
[ position_restraints ]
; ai funct fcx fcy fcz
1 1 1000 1000 1000 ; restrains to a point
2 1 1000 0 1000 ; restrains to a line (y-axis)
2 1 1000 0 0 ; restrains to a plane (y-z-plane)
so that means that i have to call differently the atoms that are in the
bourdary side that i want block?
How i can choose the parameters fcx fcy and fcz? what these value stand for?
Bests.
Il 24/04/2015 18:45, Alex ha scritto:
> Andrea Minoia's tutorial describes the setup of angles, which in the
> case of graphene, is extremely simple from the geometry standpoint. There is no need for
> "chancing," just add the proper entries under [dihedraltypes] in
> ffbonded.itp, x2top will take care of the rest.
> It's also a pretty good idea to actually read the manual on the definition of angles and dihedrals.
>
> Energy minimization destroys the sheet, because there's a mess in your
> setup.
>
> Alex
>
> MC> Hi people,
> MC> I was able to run the graphene layer sheet, by follow your advices.
> MC> I had a problem with the dihetral angle,
> MC> i solved it by chancing, im the top file the funct parameter from 1 to
> MC> 3, as reported in bold below,
> MC> .................
> MC> [ dihedrals ]
> MC> ; ai aj ak al funct c0 c1 c2
> MC> c3 c4 c5
> MC> 6 1 2 3 *3 *
> MC> 2 1 6 5 *3 *
> MC> 2 1 88 87 *3*
> MC> 1 2 3 4 *3 *
> MC> ...........
>
> MC> and also, by changing in rtp files all_dihedrals from 1 to 0,
> MC> ......
> MC> [ bondedtypes ]
> MC> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
> MC> 1 1 3 1 *0* 3 1 0
> MC> ......
>
> MC> But, when i run the mdrun file, after the minimizzation, the model
> MC> result destroyer, all the atom of graphene are spreads arround monitor,
> MC> and they are not yet connected as in the original geometry.
> MC> I would like to have some advices. What is wrong? how i have to set the
> MC> dihedral angles?
>
> MC> Thanks.
>
>
> MC> Il 23/04/2015 20:04, abhijit Kayal ha scritto:
>>> Hi Mercelo
>>>
>>> Copy the oplsaa.ff directory to your working directory. Then in
>>> ffnonbonded.itp file add the following lines..
>>> opls_995 C 6 12.01100 0.000 A 3.40000e-01
>>> 3.61200e-01
>>> opls_996 C 6 12.01100 0.000 A 3.40000e-01
>>> 3.61200e-01
>>> opls_997 C 6 12.01100 0.000 A 3.40000e-01
>>> 3.61200e-01
>>>
>>> Then in atomname2type.n2t file add the following lines.
>>> C opls_995 0 12.011 2 C 0.142 C 0.142
>>> C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
>>> C opls_997 0 12.011 1 C 0.142
>>>
>>> Then use g_x2top. This will work.
>>>
>>> On Thu, Apr 23, 2015 at 10:54 PM, Alex <nedomacho at gmail.com> wrote:
>>>
>>>> I think we've covered this when I was having the same issue. If you're
>>>> trying to simulate a multi-molecule system, then just copy the entire
>>>> forcefield .ff folder to your local directory and modify the following
>>>> files:
>>>>
>>>> ffbonded.itp
>>>> ffnonbonded.itp
>>>> atomnames2types.n2t
>>>>
>>>> No need to create rtp entries for graphene/nanotubes, so you can
>>>> ignore that part of Andrea's tutorial.
>>>>
>>>> Instead of just "C" in his tutorial, come up with a unique label
>>>> to avoid conflicts, which should then also be used in your PDB. Then what
>>>> I would do is create a topology entry
>>>> for just graphene and convert it to a stand-alone itp by stripping off
>>>> system
>>>> definitions. This is basically opening the top file, removing those
>>>> definitions and resaving as *.itp.
>>>>
>>>> After that, you can just use pdb2gmx on the remaining
>>>> parts of the system and complete the system topology by hand. I know,
>>>> this sounds like a lot of manual tweaking, but this is the paradigm.
>>>>
>>>> Good luck!
>>>>
>>>> Alex
>>>>
>>>>
>>>> MC> I run a graphene nanolayer, usin the below description (from previous
>>>> mail.
>>>> MC> Now i got an other error. It look like there is a conflict in a force
>>>> MC> field system, someone can suggest me how to modify it?
>>>> MC> the force field file came from Minoia advices, reported in the web
>>>> side!
>>>> MC> /
>>>> MC> //Program grompp, VERSION 4.6.7//
>>>> MC> //Source code file:
>>>> MC> /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line:
>>>> 752//
>>>> MC> //
>>>> MC> //Fatal error://
>>>> MC> //Syntax error - File forcefield.itp, line 31//
>>>> MC> //Last line read://
>>>> MC> //'1 3 yes 0.5 0.5'//
>>>> MC> //Found a second defaults directive./*
>>>> MC> *
>>>>
>>>>
>>>>
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>>>
> MC> --
> MC> Marcello Cammarata, Ph.D.
> MC> 3208790796
>
>
>
>
--
Marcello Cammarata, Ph.D.
3208790796
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