Re: [AMBER] Question regarding ntx and irest

From: Gustaf Olsson <>
Date: Wed, 25 Sep 2019 20:01:19 +0000

Thank you David, it makes a lot of sense.

As long as I can remember, there has never in the manual been an option "7" which means it has to be fairly old. Taking a trip down memory lane I remember someone telling me that "no, its just the sum of options 2 and 5" which did not make a lot of sense though being very green I accepted this answer even though this was not documented in the manual.

Still, now I know and I'll keep using irest=1 and ntx=5 until these settings change.

All the best

// Gustaf

Från: David Case <>
Skickat: den 25 september 2019 15:43:35
Till: AMBER Mailing List
Ämne: Re: [AMBER] Question regarding ntx and irest

On Wed, Sep 25, 2019, Gustaf Olsson wrote:
>I recently got involved in another persons project and we were going to re-evaluate some old simulations. In doing so we basically ran the old jobs though I found it interesting that there were “impossible” settings that stil ran.
>In the old files these were the settings:
> irest = 1,
> ntx = 7,
>Then I noticed
>that switching to ntx=1 produced the same exact error while using ntx=5
>produced results as ntx=7.

Nowadays, ntx=5 and 7 are identical: the code figures out if it needs
box information or not based on other information. Also, the format is
auto-detected, so the old "even/odd" distinction is no longer relevant

Bottom line, use ntx=1 to read just coordinates, ntx=5 to read
coordinates and velocities.

The irest variable determines *how* those input velocities are used: if
irest=0, even though you read in velocities, they will be ignroed; if
irest=1, the input velocities must be present (i.e. you must also set
ntx=5), and will be used to continue the simulation from the end point
of the last run.

....hope this helps....dac

p.s.: I have no real idea what happens when ntx is not 1 or 5 (which are
the only two values documented in the Reference Manaul (section 17.6.2).
We really should not be allowing any other values, although I know we
allow 7 for backwards compatibility with older versions of the code.
Also, I'd have to study code to say what used to happen in older versions.

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Received on Wed Sep 25 2019 - 13:30:01 PDT
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