AMBER Archive (2004)

Subject: Re: AMBER: MD problem (very long parhabs endless runtime)

From: Daniel Wetzler (
Date: Sun Oct 24 2004 - 04:40:09 CDT

Hi Ross,

I ran all the tests within the examples directory using
the make test.sander command.
All tests passed within some seconds without problems.

Now I will copy the files from your tutorial to my computer and try to run
the vacuum MD.

I had to include some new atom-types within my modell could this result into
a problem like mine ?

>Ok, that's fine. I suggest, however, that you look into doing a more complex
>equilibration of your system rather than just the MD scheme you have
>proposed. See the Amber DNA tutorial for an example of how to minimise a
>system and then slowly heat it and then equilibrate it. I.e. simply starting
>a system off at 300K with constant pressure can lead to instabilities. You
>would probably be better to start at 0K and ramp the temperature up to 300K
>with constant volume over about 20ps before switching to constant pressure.
>This is secondary to your problems of not obtaining any output however.
Ok, thanks for that hint. I think that's much better than my scheme.
Thank you !

>My question is though, do you 'really' want the velocities as a function of
>time. Typically people never use the velocities, they just want the
>positions and so ntwv is usually set to 0. Unless of course you have a
>specific reason for wanting the velocities.
Oh I have to admit here, that during my tries to get any output I played
with all the parameters
which could result in any output. Since I can't solve my problem without
any Errror.

Thanks for your help. Now I will try to find out what's wrong by running
through your
Tutorial MD.

Best wishes,

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