A note on distance tolerances

Distance tolerance (that is, the minimum distance between pairs of atoms of different molecules) may differ from one system to another. Particular cases that may need additional attention are:

• Coarse-grained models: of course, since the models are not atomistic, the distance tolerance desired might be larger than that generally used for atomistic systems. However, this is not always the case, as the usual tolerance may well be large enough to guarantee a proper initial packing of the system. Since version 15.133 you can use different radii for different atoms, and this can be useful in these cases as well.

• Cyclic systems: Some users have observed that with the 2.0 Angs tolerance some cyclic systems (toluene, for example) may eventually get linked during packing. If you observe that kind of behaviour, a small increase on the distance tolerance probably will solve your problem. You can also try to increase the initial tolerance by using, for example,

discale 1.5

as an additional keyword. In this case, the packing will start with a 1.5 times greater tolerance, thus probably avoiding overlaps, and will only progressively reduce the final tolerance to the actual desired value (usually 2.0 Angs).