There are variations in the way that gems are used with chakras between Vedic and Western Gem therapies. These differences are not particularly contradictory, but are differences of culture and perspective and when we enter into these subtle realms we need to be very cautious not to try and box and confine these realities into linear categories. Modern Western Gem therapy as its roots in The Egyptian Mystery schools as well as within the branches of Healing based on the Jewish Mystical Tradition of Kabbala as well as the Pythagorean Healing philosophies of Ancient Greece.
Modern physical sciences look at light and colour (which is what Gem therapy encompasses) as wavelengths, vibrations and energy. Today's scientists have proven that each color of the spectrum has its own wavelength and vibratory rate.
It would be if you had the color spectrum placed on a pyramid. The bottom would be red. The wavelengths are longer. At the top would be violet, the wavelengths shorter and the colors vibrate more quickly. So, if you would then superimpose the human body onto the pyramid. Red would interface with Muladhar and violet with Sahasrara. As with any power, the use of gems and rudrakshas indeed should be treated with respect.
I personally in the 20 years that I have used gems for myself as well as with clients for meditation aids have never had any dangerous or unpleasant results. I took the time to consult with two colleagues who also have many years of experience in this field and they too, have not had any incident to cause alarm. They have had similar experiences to what I have felt and that is if one can feel that they are being over-stimulated by a gem and if that is the case, you take it off your body. These sensations will be a feeling of agitation or being ungrounded and goes away very quickly once gem is removed from the body. As one friend put it who also does very deep cranial-sacral therapy, "It is like being near a stove, you know you are getting too close to the fire because you can feel the heat. Even a child knows if you feel the heat and get too close you will get burned.
In the case of rudraksha therapy, it has been my understanding in reading the literature and the scriptures that it is the nature of the rudrakshas themselves to integrate with the subtle body and with the kundalini in such a way that is balanced and protected, so one may wear with confidence that there will not be any disharmonious reactions. In fact, with the rudrakshas interactions with the neuro-transmitters of the brain, this in turn balances the nervous system so that there are no harsh "Kundalini experiences".
Amethyst stone for e.g. is recommend for Sahasrara as the qualities of amethyst itself are that of transmutation and so work in harmony with the power of the rudrakshas to release densities within the system that would interfere with the flow of the kundalini and in this case assist in the harmonious opening of the sahasrara.
There is a very interesting reference in the Vedic Scripture, "Shat Chakra Nirupana" which is like a guided tour of the chakras to the abode of Brahma within the Thousand Petal Lotus. This is described in verses 49-51 of the text. It is said that when this portion of the Sahasrar is opened by the Kundalini, the Yoga will hear the spontaneous repetition of the mahamantra, "Hamsa".
Since emerald and the green stones are the stones of Lord Brahma, then I would offer that it would by all means be advised to use emerald for anyone who experiences this phenomena or who is using this mantra.
Sphatik crystal is good for all chakras. Sphatik especially has that wonderful quality of being the dwelling place of Shiva/Shakti in union and of course this is the ultimate journey for all of us to have Maha Ma Kundalini come to dwell forever in the Sahasrar. Sphatik also has that wonderful cooling quality that would be very helpful if an intensity of energy is experienced. It blends well with 11 mukhi rudraksha as 11 mukhi is the Light Mass of Lord Rudra . So I offer this in the Light & Grace of Shri Saraswati, the Devi of all Knowledge & Wisdom.
Om Eim Saraswatyei Swaha
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