Re: [AMBER-Developers] force-field naming (redux)

From: B. Lachele Foley <>
Date: Mon, 9 Mar 2015 01:53:15 +0000

How about this, or similar:

* Update the tutorials to say "Please see the XYZ section of the AMBER manual for the most current force fields. For the purpose of this tutorial, we will use..."

* Then, in the AMBER manual, have a set of written-out-in-the-manual, suggested leaprc sets to source for various purposes. Then, the person has to copy those into a file (so they have to be aware of what they're doing). But, they also have some suggested recipes to make it easy for new folks.

:-) Lachele

Dr. B. Lachele Foley
Associate Research Scientist
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Ilyas Yildirim <>
Sent: Sunday, March 8, 2015 9:33 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] force-field naming (redux)

Just my suggestion: I like the idea of Ross that it will be user friendly
to include something saying (in a formal way) "Hey, if you just want to do
an MD and not worry about the ff, here is what we suggest you to load for
nucleic acids and proteins". This said, there should be something else in
the manual saying more about how to mix & match force fields. I've seen
quite some people trying to test force fields, and without a proper way of
doing that, it will be a big big hassle for them.

Best regards,

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry | University of Cambridge =
   = Lensfield Road (Room # 380) | Cambridge, UK CB2 1EW =
   = Ph.: +44-1223-336-353 | E-mail: =
   = Website: =
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On Sun, 8 Mar 2015, Ross Walker wrote:

>> On Mar 8, 2015, at 6:18 PM, Jason Swails <> wrote:
>>> On Mar 8, 2015, at 3:40 PM, Ross Walker <> wrote:
>>> I would like there to be a 'default' force field that is either:
>>> 1) Loaded by leap by default.
>>> 2) Loaded with 'source leaprc.default'
>>> This would make things a lot simpler for beginning users. Option 1 might prove troublesome since I don't know how well one can unload parameter sets in leap if you wanted to switch things out so option 2 with documentation might be optimal.
>> I think choosing a force field should be deliberate. (1) is already possible if you decide what force field you like best and name that file “leaprc”. (2) is also avoiding a deliberate choice. Deliberation reinforces the importance of choosing a force field, even if they just pick the one we suggest they use (because the act of typing “source leaprc.ff14SB” tells them what they’re using).
>> I think better tutorials (like B0 from Ben and you) are more important than providing a way of putting off (indefinitely?) learning about the concept of force field choices and selection.
> But this is my whole point. I very much think we SHOULD decide on a force field for people - At the very least we should say - if you don't know which force field to use this is what the AMBER developers recommend as the current state of the art. If you are an expert then feel free to change this but if you don't know the differences etc then this is what you should use.
> The problem with the tutorials is that it is impossible to keep them up to date - so people still see FF99SB etc and it just confuses the hell out of people.
> The way to make more people use our code is to make it as simple to use as possible. Giving people more rope than they need to hang themselves is just a bad idea. This is why Charmm is so impenetrable to new users for example.
> All the best
> Ross
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> |\oss Walker
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Received on Sun Mar 08 2015 - 19:00:04 PDT
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