AMBER Archive (2004)

Subject: RE: AMBER: saving trajectory parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Nov 27 2004 - 18:52:03 CST

Dear Ed,

> have to be run out to > 10 ns. To write out an entry to a md.crd
> trajectory file at each time step for analysis will generate
> huge files,
> even if the simulation is broken up into segments. I would
> like to avoid
> this if possible. Is there a way in Amber7 to save the
> coordinates of a
> restricted set of four atoms at every time step, while adding a new
> structure to the md.crd trajectory file at a larger increment in time?

As far as I am aware there is no feature in the code to do this but it
shouldn't be too hard to implement it yourself. See the routine corpac() in
dynlib.f - called from runmd(). This routine handles the writing of
coordinates to an mdcrd file. You could quite easily modify this to check
the step number and either write the 4 atoms you want to a file (say mdcrd2)
or write a standard coordinate frame.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

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