Objective: To analyze coexistence state and interaction among starch

pectin these two common polymer substances and small molecule active substances from water extract of traditional Chinese medicine. Method: Taking Huanglian Jiedu decoction as an example

computer simulation technology was adopted

steps as modeling of analysis materials

minimization of system energy

planning of total system energy

count of energy of common polymer materials taken alone

consideration of energy of small molecule active substances existed alone

interaction relationships with common polymer substances(starch

pectin) and small molecule active substances(berberine

palmatine

baicalin

geniposide) were analyzed. Result: Common polymer substances(starch

pectin) showed mutual attraction relationships with berberine and palmatine

showed weak mutual attraction relationship with baicalin

but there were mutual repulsion relationship with geniposide;Average interaction energy between starch to berberine

palmatine

baicalin

geniposide were -32.159

-28.630

-5.974

234.295 kcal·mol-1

respectively;Average interaction energy between pectin to berberine

palmatine

baicalin

geniposide were -19.717

-19.804

-1.067

253.258 kcal·mol-1

respectively;Separation easy degree between starch

pectin and small molecule active substances were in the order of geniposide >baicalin >palmatine >berberine. Conclusion: Van der Waals force played leading role in interaction of common polymer substances and small molecule active substances

but electrostatic interaction was small(3%-15%)

size and direction of interaction energy related with spatial location of active substance.