repel nonbonded energy function

Thu May 16 19:53:17 EST 1996

On 16 May 1996, thiel at FOREDEC.BIO.CORNELL.EDU (Dan Thiel) wrote:

>Also, regarding the model, this 
>function causes the initial VDW energy to rise to 190,000 and
>the total energy to rise to 390,000.  Is this indicating major
>problems with the model?   What value should the VDW energy be before
>I switch off the repulsive function?

Repel nonbonded energy function apply to the case of too many bad 
contacts and too high VDW energy. In this case Lennard-Jones function
may cause minimization exits. Because of the diffence of the two 
function, the corresponding values of VDW enery are different.
Once I used Repel function to releave bad contacts. When I turn on 
the repulsive function, the E(VDW) rise to 103056 and Etotal rise 
to 244181. When 15 cycles of minimizations finished, the E(VDW) falled
to 44493. It seemed still high. But when I switched off repulsive 
function and turned on Lennard-Jones fonction, the E(VDW) changed to
-573, which is already very low.


More information about the X-plor mailing list