Dear Sir/Madam,
I have done a long simulation. In order not to avoid the problem of outside box, I have used iwrap=1, in all my calculations.
However, when I do
rms first out xxx_all.rms .CA,C1
atomicfluct out xxx.bfactor byres bfactor
I found the profile is very strange. Please kindly refer to my attached excel files for the profiles.
I also need to do following analysis with ptraj, what should I do to get a reasonable profiles. It seems that when the molecule is moved to fit the box size, it affect all the analyzing parameters.
I also have to do clustering analysis and the following analysis, what should I do to solve the problem?
atomicfluct out xxx.nobfactor .CA,C1 byresaverage xxx_average_nobox.pdb pdb noboxmatrix correl .CA,C1 out xxx.corr byreshbond distance 3.5 angle 120.0 solventdonor WAT O solventacceptor WAT O H1 solventacceptor WAT O H2 out xxx.WAT.hbond2
Many thanks.
Cat
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Received on Mon Jul 16 2012 - 06:30:02 PDT
