AMBER Archive (2005)

Subject: RE: AMBER: trajectory of minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Feb 06 2005 - 12:36:29 CST

Dear Julie

> The minimization only outputs the end state structure. Is there a
> way to save the data as its minimizing? Thanks.

Not easily. Although you could modify the code in runmin to write the X
(coordinate) array to disk every step. You could do this either by calling
the standard routine for writing a restrt file (mdwrit) on every step. Make
sure you change the contents of the variable restrt before calling the
routine each time or you will overwrite the old file. One example would be
to append the value of nstep to the restrt filename. This will give you
nstepS worth of restrt file for each step.

A second option would be to call corpac on every step so that the x array is
written as successive frames to the mdcrd file.

I hope this helps.
All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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| EMail:- ross_at_rosswalker.co.uk |
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