Dear Ross:
When I finished reading your words. I cannot help to give my
appreciations for you and all those contribute to this new lipids FF.
Hopefully we general users can also provide some helps for the
development of this FF. I am also testing it for POPE these days, I will
update my comments or issue what I found.
best
Albert
On 05/11/2012 07:07 PM, Ross Walker wrote:
> Dear Vlad,
>
> Thank you. This is VERY well put and I appreciate the understanding. I'd
> like to caveat a few points if I may. Firstly there are only 4 of us working
> on this. Myself and Ben Madej at UCSD and Knut Teigen and Age Skjevik at the
> University of Bergen. This work is being done with NO specific funding and
> we are doing our best. Age is in the process of writing up his Ph.D which
> puts him mostly out of action, Ben is completing mandatory courses required
> of Ph.D students in the US and Knut and I are continually writing either
> funding proposals or report about writing reports to try to keep middle
> management and the bean counters happy. Thus I would really appreciate some
> patience here.
>
> This is a VERY large undertaking and this certainly represents the very
> first iteration of this force field and not conclusion of hundreds of man
> years of effort. We have released it now in the hope that people can try it,
> identify problems, test it widely and I hope provide constructive feedback
> and even actively help developing it such that the later iterations will
> ultimately benefit from this. There will most definitely be updates coming
> for the force field. The initial work has focused on developing a flexible
> framework that is compatible with the AMBER 'way of doing things'. The
> parameters have been taken in this first iteration from GAFF, an approach
> pioneered by Gould et al. As such these parameters are far from optimal but
> for the moment should work with NPgammaT, just don't go expecting accurate
> free energies of solvation of peptides in a lipid membrane please!
>
> We are working ourselves and in collaboration with the Gould group to refine
> the parameterization to ultimately allow NPT simulations to be run and to
> vastly improve the accuracy of the force field. For now though there are no
> golden bullets. This is a long term undertaking and this is the first baby
> step along that path. If you want to run lipid simulations you need to
> realize that these are not for the faint hearted. You need to be prepared
> when setting up such simulations to get your hands dirty. This means having
> an understanding of how the AMBER force field fits together, how leaps
> works, what NPgammaT actually means etc etc. I would very very much like to
> make these simulations simple and routine and this is the goal we are aiming
> for but we are not there yet. The modular, AMBER compatible, framework we
> have developed begins this process but is certainly not the end. Also
> tutorials are not going to be the holy grail here, these will assume a
> substantial amount of underlying knowledge about AMBER and the AMBER force
> fields so please do not expect miracles. At least not in the short term. ;-)
>
> So please do try this force field, test it out, provide us with careful
> constructive feedback, identify bugs that exist (such as the leap writepdb
> bug) but also please appreciate that we have very limited personnel and
> funding for this project. If you REALLY REALLY wish to help then please join
> a review panel and look favorably upon our proposals. ;-) Or just skip the
> middle man entirely and feel free to mail us your tax refund check. ;-) :-P
>
> Just my 3c for today.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Vlad Cojocaru [mailto:vlad.cojocaru.mpi-muenster.mpg.de]
>> Sent: Friday, May 11, 2012 7:14 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] lipid11 force filed question
>>
>> Albert,
>>
>> I think you need to be patient here ... We should probably rather be
>> happy that somebody took the burden to develop such a force field and
>> wait until it will be published and tested. Anyhow, I believe people
>> should not jump and run masses of simulations with new stuff until it
>> is
>> properly documented unless they are going to spend some time testing
>> it.
>> Also, think that the tutorials are actually a favor that is provided by
>> the developers to us, the users. So, I think we should either be
>> patient
>> or those that are really eager to work with the new ff should start on
>> their own .. At the end of the day the setup is in the spirit of AMBER
>> and the manual describes it a bit, therefore somebody experienced with
>> AMBER could start settings systems without any tutorial.
>>
>> Having said that, I think it would be great to see how well the new ff
>> reproduces lipid properties in the NPT ensemble ... I would rather wait
>> for this before blindly starting lots of simulations with the new ff
>> ...
>>
>> Vlad
>>
>>
>> On 05/11/2012 03:58 PM, Albert wrote:
>>> It seems that lots of people are highly looking forward to this new
>> FF
>>> for lipids in Amber. Unfortunately, few comments were obtained from
>> the
>>> developer.... Also the tutorial is also delayed for such a long time
>> and
>>> it doesn't released yet at present...
>>>
>>>
>>>
>>>
>>> On 05/11/2012 02:34 PM, Jason Swails wrote:
>>>> Please only send one email with the topic (you sent 4 within the
>> span of a couple hours). The lipid11 force field developer is typically
>> fairly responsive on this list and you should receive an answer within
>> a reasonable period of time.
>>>> Also remember that oftentimes the responders are in a different time
>> zone than you are -- at the time of your first email they were very
>> likely asleep for the night and have probably still not woken.
>>>> All the best,
>>>> Jason
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 11 2012 - 11:00:06 PDT
