AMBER: md's

From: yen li <>
Date: Mon, 6 Dec 2004 08:08:07 -0800 (PST)

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.

Do you Yahoo!?
 Take Yahoo! Mail with you! Get it on your mobile phone.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Dec 06 2004 - 16:53:00 PST
Custom Search