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 <nedoma...@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> Marcello Cammarata, Ph.D.
MC> 3208790796
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