Re: [AMBER] Error when running MD

From: David Case <>
Date: Fri, 13 Dec 2019 18:42:10 +0000

On Fri, Dec 13, 2019, maya nair wrote:

>I am trying to do a nmr refined MD simulation. Minimization was done for
>the system without any error. When doing MD with the protocol
>simulated annealing protocol, 20 ps
> &ewald
> eedmeth=5,

Do you really need eedmeth=5 (1/r dielectric)? This is an
old-old-old-old option, dating back to the days when computers were so
slow that taking a square root seemed troublesome.

I'd really recommend using an igb option, like igb=8 (for modern Amber
protein and nucleic acid force fields.) The problem you are seeing with
box sizes goes away then. Or, if you want a "vacuum" force field (also not
recommended!), set igb=6.

[I see that there is an example script in the Reference Manual (p.
553) that sets eedmeth=5. It's discouraging how easy it is for
developers to fail to update examples as time goes by....I'll get that fixed,
but please consider setting igb=8 instead.]

...good luck....dac

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Received on Fri Dec 13 2019 - 11:00:02 PST
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