Hi,
You will need to have both ffbonded.itp and ffnonbonded.itp .
atomname2type.n2t is needed for g_x2top to make it work correctly.
Good luck.
-Alex
On 26/11/2017 10:52, Rakesh Pant wrote:
Dear, Alex
Does it mean, we do not need to define all the atomtypes in the .nt2 file.
It is enough to define all types in bonded and non-bonded itp.
Thanks,
Rakesh
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On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin <nased...@chalmers.se>
wrote:
Edit the content of you ffnonbonded.itp file approximately this way:
[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
C 14 12.00 1.08 A 0.44000 0.63 ;
OCE 8 15.999400 -0.70 A 0.35400 0.159705 ; C-O-C
Bridging Oxygen;
OCH 8 15.999400 -0.51 A 0.35400 0.159705 ; C-O-H
Oxygen;
HCO 1 1.008000 0.32 A 0.04490 0.235725 ; H-O-C
Hydrogen;
....
You would need to search literature for respective ff parameters: all the
above parameters are taken from another topology to give a template.
-Alex
On 26/11/2017 10:37, Rakesh Pant wrote:
Dear Alex,
If I use O atoms to define the respective functional groups, then how to
include the C atoms present in the molecule.
Thanks,
Rakesh
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On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin <nased...@chalmers.se>
wrote:
Hi,
As I understood the problem, you need to distinguish between surface and
buried carbons?
You could define two atomtypes that differ in name and use it to process
with x2top.
Below is an example of *.n2t lines. You would need to change the charges
and bondlengthes.
...
O OCH -1.05 15.9994 2 C 0.154 H 0.1 ; oxygen, -OH
group
O OCE -1.05 15.9994 2 C 0.154 C 0.154 ; bridge
oxygen
...
Then you need *.n2t file in your ff.
Good luck!
-Alex
On 25/11/2017 22:06, Justin Lemkul wrote:
On 11/25/17 3:31 PM, Rakesh Pant wrote:
But then I how will include the C atom (which is also one of the
atomtypes)?
No idea, but I know people on this list have dealt with graphene oxide
before, so hopefully someone else chimes in.
-Justin
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