AMBER Archive (2006)

Subject: RE: AMBER: minization: outputing intermediate snapshots

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Feb 14 2006 - 12:34:30 CST

Dear Vlad,

> I was wondering if there is any way to output intermediate coordinates
> during a minimization run.... I looked at setting ntwr<0 but
> it did not
> produce any rst output..
>
> Does anybody know how to do this?

I don't believe that there is any facility in the code to do this, however
you could create a script to do it yourself.

Say you wanted to run 1000 steps of minimisation and you wanted the
intermediate structure every 50 steps.

You could create an input file to run 50 steps of minimisation and stop.
This would then create a rst file after those 50 steps. You could then write
a script to simply run your minimisation in 20 x 50 step blocks with each
step using the rst file from the previous step as the initial geometry.

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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