On Thu, Dec 11, 2003, A. Hungie wrote:
>
> My system contains 800 atoms of DNA, 20 Na+ ions and 10500 atoms of water
> molecules (total 11320 atoms). The 7 ps MD trajectory stored coordinates of
> all atoms every 2 fs (total 3500 snapshots). The trajectory contains only
> coordinates, without velocity. I would like to calculate vibration
> frequency of only DNA. Someone has suggested me to run trajectory through
> PTRAJ and average DNA structure. Therefore, in file "average.pdb" contains
> only DNA without solvent and counter-ions. My questions are as follow.
>
> 1. to run quasih, it should be
> quasih -nat # -f # -x xyz [-novec| -v vecs] -first # -last # -lastvec
> For number of atoms "nat", what should I put? 800 or 11320?
800; note that quasih creates the "xyz" file of average coordaintes...you
don't need to make such a beast yourself. But you *do* need to run the
trajectory throught ptraj to both strip the solvent and to superimpose the
frames onto a common overall coordinate frame. Also, you need to create
a "mass" file (missing in your description above).
There is a test calculation in amber7/test/quasih, which may help you see
how things are supposed to work.
>
> 2. If nat=800, do I have to extract coordinates of DNA from trajectory
> (delete coordinates of solvent)? If I have to delete coord of solvent,
> should I also delete size of simulation box inserted between each snapshot?
yes, yes (respectively to your two questions)
>
> 3. Do trajectory storing coords every 2fs and trajectory storing coords
> every 500 fs give the same vibration frequency?
no; for long enough trajectories, the results should be close.
..dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Jan 14 2004 - 15:53:08 PST
