Dear All,
I have simulated nucleic systems with ions using NAMD. I am trying to
calculate msd values of ions using ptraj in order to further calculate their
diffusion coefficients from the simulations. There are about 10 ions of my
interest. I have calculated their msds, but the plots are not showing
linear behavior as they should.
There are 2+N columns for the data. (N number of atoms in mask), where the
first is time and the second column which as far as I could make out is the
average of all the other columns. Please correct me if I am wrong.
Only the second column as average of the msd of mask atoms is showing a
linear behavior. But msds of the atoms of interest (no doubt in increasing
order) are spiky, irregular, with very small linear behavior inbetween. I am
attaching a pdf of this graph where the average of all mask atoms (in black
color) and graph of one ion (in red color). What could be the reason, I may
be missing something!!!
I have tried doing with and without imaging. Also tried using unwrapping the
trajectory (using pbctools of VMD), but still cannot figure out where the
problem is?
> ptraj.in (without imagidin)
trajin inp.dcd
diffusion ":SOD,POT,MG" 2 outnoimg
> ptraj.in (with imaging)
trajin inp.dcd
center :2-173 mass origin
image origin center byre ":SOD,POT,MG" com: 2-173
diffusion ":SOD,POT,MG" 2 outimg
Please help.
Thanking you,
Regards
Monika
--
((¯`·_.·[Monika]·._·´¯))
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Received on Fri Feb 26 2010 - 22:30:02 PST
