Is it "using an MD simulation" or "using a MD simulation"? MD stands for "Molecular Dynamics".
Since "M" is pronounced "EM", I thought it must be "an". I found both usages on the web through searching in Google.
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It is one of the extremely rare universal rules of English: the indefinite article an is used with words that begin with vowel sounds, and a with words that begin with consonant sounds. Note that this is a pronunciation rule, not a spelling rule, thus
As a consequence, the expected article may differ depending on region or dialect.
Whether a MD or an MD is appropriate therefore depends on how MD is to be pronounced. If it is an initialism, em dee, then an MD is correct. If it is an abbreviation meant to be read out in its long form, then a MD could be correct, as in a Maryland or a medical doctor.
Sometimes, there is no agreement on how to pronounce a word or abbreviation, and both variants can be found in use: