HI Albert,
You are right ...
Be reminded though that the 2 force fields behaved best for DE SHaw and
coworkers for the systems they studied !! This does not imply that the
same ff will be equally good for systems of completely different nature.
The lipids in your system add a level of complication for your choice
... There were recently lots of discussion on the new gaff-based and
lipid11 force fields for lipids. ...
In principle, there shouldn't be any incompatibility issues between gaff
and ff99-based force field versions ..
CHARMM36 for lipids has been around for a while and it seems to behave
well in the hands of different groups.
So, I would say tough choice. Maybe you could get in touch with the
CHARMM developers to discuss the compatibility between different CHARMM
ff versions ... There should be a CHARMM36 version for proteins, isn't
it ? If yes, were the problems with CHARMM27 solved ?? I am not
experienced with CHARMM ff.
Best,
Vlad
On 11/21/2012 03:36 PM, Albert wrote:
> Hi Vlad:
>
> thanks a lot for such kind comments again.
>
> I've read that PLOS ONE paper before, in that paper, the author from
> Deshaw group finnally conclude that the CHARMM22star and Amber99ILDN are
> the two best FF for long time scaled MD simulation. However, my system
> is a membrane/protein one, and I've asked people in charge of
> CHARMM22star FF, and he told me that they didn't validate the
> compability between CHARMM22star and CHARMM36_lipids FF. Of course for
> Amber FF, I hope it won't be a problem for the compability between
> AMBER99SB-ILDN and AmberGAFF FF.
>
> If am right, both AMBER99SB-ILDN and CHARMM22star FF were devoloped
> in Deshaw group instead of AMBER or CHARMM group.
>
>
> best
> Albert
>
> On 11/21/2012 03:21 PM, Vlad Cojocaru wrote:
>> See also
>>
>> Lange, Spoel and de Groot, Biophys. J. 2010
>>
>> From the NMR-based modifications, see
>> Li, .. Bueschweiler, Angewande Chemie Intl Edition 2010
>>
>> Also, ff12SB could be interesting to follow but it is not published yet
>> ... However, on this list people have reported successful long
>> simulations ...
>>
>> Best wishes
>> Vlad
>
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--
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
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Wed Nov 21 2012 - 07:00:04 PST
