Crystallographic refinement based on molecular dynamics (MD) has been applied to a 2.5 A resolution X-ray structure of the pore-forming fragment of colicin A. The crystallographic R factor was reduced from 48 to 23% with a concomitant improvement in stereochemical parameters. The method considerably speeded up the refinement process but was associated with some pitfalls. In particular, some badly fitted segments of the structure required manual rebuilding, even after MD refinement and some problems with weighting schemes were encountered. Analysis of the effects of the refinement and ideas for improvements are presented.