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
Hi people,
I was able to run the graphene layer sheet, by follow your advices.
I had a problem with the dihetral angle,
i solved it by chancing, im the top file the funct parameter from 1 to
3, as reported in bold below,
.
[ dihedrals ]
; aiajakal funct
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
I run a graphene nanolayer, usin the below description (from previous mail.
Now i got an other error. It look like there is a conflict in a force
field system, someone can suggest me how to modify it?
the force field file came from Minoia advices, reported in the web side!
/
//Program grompp,
Hi Mercelo
Copy the oplsaa.ff directory to your working directory. Then in
ffnonbonded.itp file add the following lines..
opls_995 C 612.01100 0.000 A3.4e-01
3.61200e-01
opls_996 C 612.01100 0.000 A3.4e-01
3.61200e-01
opls_997 C
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
Thanks Justin, and thanks Alex.
If i have run the command x2top using pbd file but i got the same error.
which files have i substitute to my version ( Gro5.0) with the ones from
the pre-5 version?
Alex did you change something in your version? i am in ubuntu OS.
/GROMACS: gmx x2top,
On 4/23/15 4:24 AM, Marcello Cammarata wrote:
Thanks Justin, and thanks Alex.
If i have run the command x2top using pbd file but i got the same error.
which files have i substitute to my version ( Gro5.0) with the ones from the
pre-5 version?
The command is the same; if you're getting a seg
Hi,
i am trying to model a Graphene nano sheet GNS on Gromacs-
I follow the advices about the nanotubes presented in the help site.
_http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_
I run this command to greate the topology:
_g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_
I
Hello,
The forcefields for CNT and graphene are identical (for the purpose of
this discussion). Two questions:
1. Where did you get the initial graphene structure?
2. Are there any CONECT statements in it?
I assume you used Andrea Minoia's guide and the contents of your
cnt2_oplsaa.ff directory
Justin, everything works for me with graphene/x2top under the latest
version. Am I doing something wrong? :)
On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/22/15 7:22 PM, marcello cammarata wrote:
yes, i used the Minoia tutorial,
i use a cnt_oplsaa at the first
On 4/22/15 7:22 PM, marcello cammarata wrote:
yes, i used the Minoia tutorial,
i use a cnt_oplsaa at the first attempt, and forward i copied and modify the
standard oplsaa folder. with both of them i have the same trouble.
The seg fault will always occur with version 5.0.4; there is a bug
yes, i used the Minoia tutorial,
i use a cnt_oplsaa at the first attempt, and forward i copied and modify
the standard oplsaa folder. with both of them i have the same trouble.
The inizial graphene layer was created using*VMD modelling toolbox*,
that was a .pdb file, i convert it in .gro
You don't need to run x2top on the GRO file, you can apply it directly to
the PDB. It seems like the PDB to GRO conversion destroyed the coordinates
due to poor formatting of the initial coordinates. This has nothing to do
with the forcefields or graphene, you may just have a crappy PDB.
Alex
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