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.
According to the previous comments I added the "center and image origin" to the ptraj run (1-677 represent all the protein 677 protein residues)
trajin ./xxx.mdcrdcenter :1-677 originimage origin center familiartrajout yyy.netcdf netcdf .N1,CAradgyr out yyy_all.radgyr.datrms first out xxx_all.rms .CA,C1
atomicfluct out xxx.bfactor byres bfactoratomicfluct 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
I found the profile is still strange. e.g the rmsd jump up and down to a very large values. It seems that when the molecule is moved to fit the box size, it affect all the analyzing parameters.
Please kindly instruct if I have using the ptraj commands wrongly. Many thanks.
Many thanks.
Cat
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Received on Tue Jul 17 2012 - 20:30:02 PDT
