Re: [AMBER-Developers] ntb vs ifbox?

From: Jason Swails <>
Date: Tue, 6 Dec 2011 16:10:33 -0500

On Tue, Dec 6, 2011 at 12:06 PM, Yong Duan <> wrote:

> Jason and Ben,
> Forcing users to edit prmtop is of course a bad idea.
> But, for the very few who wants to use ntb=0 for systems of ifbox=1 (or
> ntb=1 for ifbox=0), they'd better know what they are doing. If a first
> year grad student does that, it is extremely likely an error.

It may be likely to be an error, sure. I included a pedagogical example of
why this may be desirable, but included it at the end of the email for
brevity's sake.

What's wrong with setting the default ntb value to be a function of IFBOX
and ntp, but allowing someone to easily override the default and set ntb=0
for an IFBOX=1 topology? In the manual, we will fully describe the
behavior (and say deviating from the default is for advanced use *only*).

But again, since PBC is not really a feature of the force field used to
parametrize a system, I don't think that function should be controlled
exclusively by the topology file (it seems too much like an awkward hack to

I'll whip up an example of what I'm talking about.

For those
> well-trained and highly innovative minds, editing prmtop is a piece of
> cake. If not, they probably should stay away from inventing new chemistry.

I only think that applies to people quite familiar with Amber. A highly
innovative or clever mind trained in CHARMM or GROMACS is probably clever
enough to keep the prmtop as far away from a text editor as possible until
they become a lot more familiar with it. How do we tell people what parts
of the prmtop are "editable"?

All the best,

Pedagogical example:

"Here's a water droplet containing a protein. Let's simulate that water
droplet in a vacuum (or in the gas phase), and see what happens. Water
droplets leave via an evaporative process. So we will impose PBCs to
simulate the bulk solution phase (change ntb to 1), now what happens?"
 That is, IMO, a useful pedagogical tool that would require users to set
ntb=0 for a periodic system, and not a situation in which you would want
prmtop hacking to be the appropriate course of action. (Just an example
off the top of my head)

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Dec 06 2011 - 13:30:03 PST
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