[gmx-users] help on Graphene Nano Sheets
nedomacho at gmail.com
Fri Apr 24 18:45:18 CEST 2015
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
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> [ 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> and also, by changing in rtp files all_dihedrals from 1 to 0,
MC> [ bondedtypes ]
MC> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
MC> 1 1 3 1 *0* 3 1 0
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> 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
>> opls_996 C 6 12.01100 0.000 A 3.40000e-01
>> opls_997 C 6 12.01100 0.000 A 3.40000e-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
>>> 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
>>> 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!
>>> MC> I run a graphene nanolayer, usin the below description (from previous
>>> 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
>>> 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:
>>> 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.
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