[gmx-users] changing form of nonbonded force fields

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 25 09:17:23 CEST 2006

Mark Abraham wrote:
> Andre Ghizoni wrote:
>> Dear gromacs users,
>> I would like to know how and if it is possible to change the form of 
>> the lennard jones potential in gromacs.  What I want to do is shift 
>> the LJ function some R radius to the right for one species, i.e. 
>> f(r-R).  In effect my potential is f(r)=C1/(r-R)^12-C2/(r-R)^6, where 
>> r is the true distance between particles.  If it is not possible to do 
>> that, I would appreciate any suggestions on approximating this 
>> function with other functions that gromacs uses.
> If I recall correctly, you might be able to do this with a table lookup 
> for LJ, however at the moment you can't use the table for only one 
> species. Some source code hacking might change that fairly readily.
actually you can, you can define one table per interaction in the matrix.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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