Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies

From: David A Case <>
Date: Wed, 9 Mar 2011 11:54:27 -0500

On Mon, Mar 07, 2011, Andrew Jewett wrote:

> If the amber community is considering
> adding new features to AMBER, then please consider the following:
> i) The ability for a covalent bond to cross the periodic box boundary.

This is likely to happen.

> ii) The ability to allow pressure rescaling in only the Z direction.
>    (while preventing rescaling in the XY directions, or visa versa).

This sounds almost like a two-line change to the code -- have you considered
trying it out?

>  a) Harmonic restraint anchor points are not fixed during NPT simulations,
> but are scaled.  It would be useful to make this optional
>    (both for belly and harmonic restraints).

See comment above.

> b) Arguably, constraints cause the virial to be calculated incorrectly.
> This can force the box to expand to a huge size.

What kind of "constraints" are you using? Do you understand what is going on,
e.g. why there is a bubble only on one side of the central slab?


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Received on Wed Mar 09 2011 - 09:00:09 PST
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