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I like to apply harmonic constraints on all c-alpha atoms during MD-vacuo, with a condition apply to maintain inter c-alpha atom distance should be less than or equal to certain threshold (eg:9 Angs) during the integration.

Are there any method exist to call harmonic constraints for the above mentioned condition.

Appreciate your help


Not exactly.

There is CONS HARM BESTFIT, which applies a restraint force for an RMSD best fit to a set of atoms (e.g. Calpha), allowing for translation and rotation; see cons.doc for details. You'd probably have to tune the restraint force to keep the deviations within some threshold value.

You can use multiple restraint sets applied to secondary structure elements or protein domains, but the atom selections should not overlap; a given atom can only be in one harmonic restraint set.
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