[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

[Alex]

Hey Justin,

Thanks. I am not entirely sure I understand your suggestion, because
this will clearly work if nothing else is added to the system (it
seems to be equivalent to that CNT guide). The problems start after I add
water, i.e. "duplicate [ defaults ]" from grompp and such. In the meantime, I will
try the earlier suggestion and add the bonded definitions on top of
what was suggested.

Alex


JL> For this, the cleanest approach is to create a custom force field, and its
JL> contents should be rather simple - bonded and nonbonded parameters for some C
JL> type (for the CNT) and whatever solvent type(s) you need.  It's actually a very
JL> bare-bones force field.  The proposal before about using values from OPLS-AA is
JL> a good guide; these are the things you need to define.  In reality, this could
JL> all be in one file:

JL> [ defaults ]
JL> ...whatever...

JL> [ atomtypes ]
JL> ...whatever...

JL> [ nonbond_params ]
JL> (if needed)

JL> [ bondtypes ], [ angletypes ], [ dihedraltypes ], ...

JL> Then create the .n2t file for creating the CNT.  That part is the easiest of all
JL> of it since everything is (should be) equally spaced. :)

JL> -Justin