Re: [AMBER] Soft-core questions for TI method

From: David A Case <>
Date: Mon, 7 Oct 2013 08:21:19 -0400

On Mon, Oct 07, 2013, yuandandan wrote:
> Checking for mismatched coordinates.
> WARNING: Local coordinate 1246 differs from partner coordinate 1246 !

> Also, I found that the output files of minimization (.out) were finished normal, however,
> the coordinates of common atoms didn’t keep the same in 0 and 1 when compare the
> two output .rst files, and then the equilibrium failed.

This is all correct, but you cannot do what you are proposing: that is, you
cannot separately minimize the V0 and V1 systems, since then the coordinates
of common atoms will not exactly match each other. If you need to do
minimization, you must do it in a TI sense, with a mixed potential, i.e. with
input files that look exactly like the ones you would use for MD, except that
you set imin=1.

...good luck..dac

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Received on Mon Oct 07 2013 - 05:30:07 PDT
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