GROMACS version: 2016
GROMACS modification: No
I was troubled with how to used the Buckingham function for nonbonded interaction. As we all know ,the LJ has two parameters such as epsilon and sigema ,however the Buckingham has three parameters A\B\C.I don’t konw how to apply the Buckingham function or just revision the Buckingham function to L-J function…Some workers had said that to use the table potential.I have learn the manuel.but do not know how to make the systerm to invoke the table.xvg .
Hi,
Buckingham potential for non bonded interaction is implemented in GROMACS see:
Table 13 in the link below show you the syntax that you have to use to define such a potential in the topology files
best regards
Alessandra
I am really appreciate for your reply, and I have followed the manual to define the potential. but it doesn’t work . I have tried with the OPLSAA forcefield, and here is the steps :
1、set the parameters of the forcefiled.itp file at the defualt part
[ defaults ]
；nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
2 1 no 0.5 0.5
2、then at the same root bulit the table.xvg files of all the atom pairs.used the parameter B of buckingham to produce the three function combined to the table.xvg files. here was seven colum datas of r, f®, −f’®, g®,−g’®, h® and −h’® ,and r 's value range was[0,r_cut off +1]
3、went to the ffnonbonded.itp files to write the AC parameter of buckingham in form of epsilon and sigema.
But Gromacs send the error that:Generating pair parameters is only support with L-J nonbonded function.
I really puzzled with that . it means that this forcefield just appropriate to L-J nonbonded interaction?
thank you very much !
Hi,
The combination rules option (in forcefield.itp) is only for L-J parameters.
When you use a Buckingham potential (func 2) you should define all the pairs in the directive [ nonbond_params ] in ffnonbonded.itp. To generate such parameters you have to use the Buckingham combination rule given here http://manual.gromacs.org/current/reference-manual/topologies/parameter-files.html#nbpar
This should resolve your error message
Finally, I do not follow why you generate tabulated potentials. If a functional form is already implemented, you do not need to generate tabulate potential. But maybe I am missing something.
best regards
Alessandra