Hello all interested in the Lipid 11 force field tutorial,
My focus has been entirely on refining/testing the parameters for the Lipid
force field so my planned tutorial got pushed back to lower priority. The
tutorial has been delayed until I get a chance to update and release it.
Ben Madej
Walker Molecular Dynamics Lab
-----Original Message-----
From: Albert [mailto:mailmd2011.gmail.com]
Sent: Monday, June 25, 2012 10:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] R: strange POPC under lipids 11 FF
I believe many people are eagerly looking forward to that. The
parametrization is definitely the most important thing for a FF.
However, it also would be important if someone can start to write a
dedicated tutorial for this FF. eg: how to build a membrane system, how to
equilibrate the whole system and so on. I also use other MD tools before, to
be honest, the tutorial and manual is not as clear as the other tools.
Probably someone can consider learn from other MD tutorial so that it would
be more clear to the users.
best
Albert
On 06/25/2012 07:14 PM, Benjamin Madej wrote:
> I'd like to add to this discussion:
>
> As many of you know, parameterization is a task that is expensive in
> time and computational resources. The goal is to assemble appropriate
> parameters for the lipids so that we have a reasonable force field
> that is fully compatible with the other Amber force fields.
>
> We've submitted the Lipid11 force field paper, and it's still in review.
> What's important about Lipid11 is that it established a reasonable
> (modular) framework for further parameterization. The paper has a
> description of the new charge derivation for the phospholipids that was
released with Lipid11.
> With the framework of Lipid11, we have a strong foundation for further
> refinement and re-parameterization.
>
> We are currently re-parameterizing several other parameters of the
> force field. However, the parameter fitting and testing takes a long
> time. The testing process is the most time-intensive task so that we
> can really evaluate how the parameters affect lipid bilayer systems.
> It's good to have other people already testing the current parameter
> set and seeing what it can do.
>
> We will release updates as soon as we have evidence that they are
> appropriate for the phospholipid systems we're all looking at.
>
> All the best,
> Ben Madej
> Walker Molecular Dynamics Lab
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Received on Mon Jun 25 2012 - 12:00:02 PDT
