[gmx-users] truncated LJ potential

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 10 14:04:34 CET 2011

On 2011-01-10 13.39, Makoto Yoneya wrote:
> Dear GROMACS experts:
> I'd like to use a modified Lennard-Jones potential (smoothly truncated at
> only the repulsive part) in the following.
> V(r)
>    = 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 - (1/4) } for r<=
> 2^(1/6)*sigma
>    = 0 for r>  2^(1/6)*sigma
> Which routine should I change to realize this LJ potential modification
> without any side effects.
> I'd like to use this in some coarse-grained simulations.
> Sorry if this is a FAQ.
> Thank you for advance.
> Makoto Yoneya, Dr.
> AIST, Tsukuba
> http://staff.aist.go.jp/makoto-yoneya/
Dear Makoto,

please look into gromacs' table potential functionality, it is described 
in the manual, and you won't have to program anything
UNLESS the sigma is different for different atom pairs, in that case I'm 
not sure if it will work.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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