[AMBER] Doubt in atomicfluct usage

From: Asmita Gupta <asmita4des.gmail.com>
Date: Tue, 6 Dec 2011 23:27:56 +0530

Dear users,

I am trying to calculate atomic fluctuations in following two ways,
but getting two sets of different values for positional fluctuations.
can anybody please explain why this is happening?

1. first calculated an average structure, rms fit to it followed by
atomicfluct {byres} in single ptraj run like:

rms reference average.pdb out filename
atomicfluct out res_fluct_avg.dat :1-34 byres
atomicfluct out at_fluct_avg.dat .1-1099 byatom
atomicfluct out backbone_fluct_avg.dat .P,O5',C5',C4',C3',O3'

2. doing rms fit and atomicfluct in separate runs of ptraj


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Received on Tue Dec 06 2011 - 10:00:03 PST
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