AMBER Archive (2004)

Subject: AMBER: question about md's

From: yen li (
Date: Fri Dec 10 2004 - 09:27:39 CST

Hi amber,
I want to clear a doubt regarding md that if i am performing a simulation(explicit or implicit) over a native protein which is obtained by NMR(which are less reliable structures as compared to X-ray), how long should i simulate in such a case. lets say i am doing for 500 ps, then can the structure after 500ps be the representative of the native and then if i want to compare the rmsd of this structure with some other structure, should i take this 500ps structure or the initial structure. Also i have learnt that for calculating energies averages over the trajactory are performed, but if i want to compare the structures(for which i have to calculate rmsd's) should i rely on the last structure or the whole trajactory.

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