On Mon, Sep 30, 2013, Vijay Manickam Achari wrote:
>
> I am trying to calculate the rotational diffusion for exocyclic group
> for sugar units where the sugars are arranged in a bilayer structure.
The rotdif command only works for a full molecule undergoing rotation in
solution. You cannot use it for just parts of a bigger molecule. [If you
fully grasp what the rotdif command is doing, you might get some interesting
information from the command you tried, but the reported diffusion tensor
would not be directly useful.]
>
> rotdif nvecs 1000 ref .C15,C16,O16,H16 \
> ncorr 90 ti 0.0 tf 0.80 dt 0.002 deffout deffs.dat \
> itmax 500 tol 0.000001 d0 0.03 order 2 \
> outfile rotdif.out
>
> Error: Rotdif: 'dt <timestep>' must be specified and > 0.
Dan may have to respond to this one.
...dac
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Received on Mon Sep 30 2013 - 05:30:05 PDT
