A few more points...
"Ofcourse you scale the coordinates!"
CHARMM allows for both scaling and non-scaling of the coordinates as a options. There are many situations where scaling coordinates is not appropriate. CHARMM uses a general symmetry operator, so we even handle the cases where there is rotational or inversion symmetry (e.g. asymmetric unit cells) and for both finite and infinite (1-D, 2-D, and 3-D). All crystal groups are supported.
Code has been well tested with a "TEST FIRST" command which compares forces and virials with changing box sizes and atom positions using finite differences.
What we lack with our method is the ability to compute pressure profiles in slabs. For example, we cannot calculate pressure changes as a function of the z-coordinate as one goes through a lipid bilayer.
Literature where we've published stuff relating to this discussion:
Pastor RW, Brooks BR, Szabo A. An analysis of the accuracy of Langevin and molecular dynamics algorithms. Molecular Physics. 1989;65(6):1409-1419.
SE Feller, Y Zhang, RW Pastor and BR Brooks. Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 1995 103(11).
Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84.
BR Brooks, CL Brooks III, AD Mackerell, Jr, L Nilsson, RJ Petrella, B Roux, Y Won, G Archontis, C Bartels, S Boresch, A Caflisch, L Caves, Q Cui, AR Dinner, M Feig, S Fischer, J Gao, M Hodoscek, W Im, K Kuczera, T Lazaridis, J Ma, V Ovchinnikov, E Paci, RW Pastor, CB Post, JZ Pu, M Schaefer, B Tidor, RM Venable, HL Woodcock, X Wu, W Yang, DM York, M Karplus. CHARMM: The Biomolecular Simulation Program. J. Comp. Chem. 2009; 30(10):1545.
You can find active links (both pubmed and journal) to these papers at:http://www.lobos.nih.gov/cbs/publications.shtml