[gmx-users] Combining two Non-bonded potentials

[David van der Spoel]

On Wed, 9 Jan 2002, Mehmet Suezen wrote:

>Form of a potential that I was using with another MD program (which I
>had
>problems with parallelization) and intent to use this form in Gromacs:
>
>Vij(r) = qi*qj/r + Aij*exp(- Bij*rij)- Cij/rij^6 + 4*eij(
>(sij/rij)^18-(sij/rij)^6 )
>
Basically you have only one extra term:
4 eij (sij/rij)^18 
as you can write
Cij' = Cij + 4 eij sij^6

It seems that you have just added an extra repulsion, possible to prevent
the singularity at rij=0 in the Buckingham potential. One can of course
ask what is the physical basis for such a potential?

There is no straightforward way to implement this in gromacs. One would
have to modify the inner loops, and pass an extra parameter to them (which
needs to be read in grompp etc.)

Your best bet is still to fit your potential to an arbitrary form that can
be represented by the gromacs table form (or better still to a normal
buckingham)

>;[ nonbond_params ] ; if there is a table what should I write in funct
>column.
>; where I do know a, b and c parameters.
> ai    aj      funct   a       b       c  
>  1     1 
>  2     2
>  1     2
O	O	1	1e-6	1e-3
C	C	1	1e-6	2e-3
O	C	1	1e-6	1.41e-3

You can also put the params in the [atomtypes ] section and use
combination rules.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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