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
-----Original Message-----
From: Vlad Cojocaru [mailto:vlad.cojocaru.mpi-muenster.mpg.de]
Sent: Friday, June 22, 2012 2:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] R: strange POPC under lipids 11 FF
Albert,
I think I have commented on your pushing attitude before but this message is
really not OK.
As long as you depend on other people, please allow these people to their
work properly. If you want things to go fast, please do the parameterization
yourself but be sure what you are doing is not influenced by your wish to
have everything done fast.
I am quite annoyed by this "fast fast" attitude which many times is
detrimental to science, people trying to do things fast and dirty just
because its a competitive world ... I prefer longer but more solid studies.
Sorry for this comment, but I think messages such as yours do not belong on
this list ..
Best,
Vlad
P.S. Thanks very much to all the people doing the lipid work. It looks like
soon we will have an AMBER-compatible force field for lipids and that's
great. Please take your time and test carefully your lipid parameters so
that people benefit from a solid study. Maybe the force field should have
not been released with AMBER12, but this is another discussion.
On 06/22/2012 10:50 AM, Albert wrote:
> well, the problem is that many people are waiting for this for such a
> long time (myself looked for it for at least half year since AMBER12
> doesn't come out and many people are talking about it that time). How
> long should we wait, this is a problem. It is quit competitive world,
> probably many people are losing their patience.....
>
> best
> Albert
>
> On 06/22/2012 10:50 AM, Gould, Ian R wrote:
>> Dear All,
>>
>> We are awaiting the response to our revised manuscript of our
>> GAFFlipid paper which we will be combining with lipid 11, work done
>> in conjunction with Ross Walker, where we get very good agreement
>> with experiment for POPC, with no surface tension term. I have
>> attached one of the tables and one of the figures from the paper
>> which give an illustration of how good the parameters are at
>> reproducing experiment. When the paper has been accepted for
>> publication we will make the parameters available to the community.
>>
>> Cheers
>> Ian
>>
>> Women love us for our defects. If we have enough of them, they will
>> forgive us everything, even our intellects.
>> Oscar Wilde,
>>
>>
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>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine Department of Cell and
Developmental Biology Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Mon Jun 25 2012 - 10:30:03 PDT
