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

From: Jason Swails <>
Date: Sun, 8 Mar 2015 21:18:10 -0400

> 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.

> I would suggest it be:
> source leaprc.ff14SB
> source leaprc.gaff
> source leaprc.GLYCAM_06j-1
> source leaprc.lipid14
> loadamberparams frcmod.ionsjc_tip3p
> This would be good since it will also give us early warning in the future of atom type clashes, incompatibilities etc.

I’m not sure that I follow here. How would we get said warning? Does tleap print something I’m not aware of?

> Does it make sense to make TIP3P with ionsjc the default water model and ion parameters? - These are probably the most commonly used.

I don’t like how we currently do water and ions. The water model and ion parameters go hand-in-hand -- they are tuned for each other. I think we should specify the water model we want to use just like we specify the ion model we want to use. But picking TIP3P also brings in the best TIP3P ion parameters. Same for TIP4PEw, SPCE, etc. As it is now, we have a default water model, but no default ions. We bring in solvents.lib (all water residue templates), but make people source a different frcmod for other than TIP3P. I personally don’t have trouble keeping it straight because I’m so familiar with it, but it’s very inconsistent.

> What do people think?
> Then we just have a 'quickstart' section as it were in the manual (and we update the tutorials to use this default) and then in the future we can update this with whatever is the latest set of force fields we recommend.

I like the quickstart, which is basically making our documentation better and clearer.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Sun Mar 08 2015 - 18:30:04 PDT
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