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
On 11/21/2012 03:13 PM, Vlad Cojocaru wrote:
> Hi Albert,
>
> We are using at the moment the AMBER ff99SB+ILDN+NMR-based
> modifications (the latter coming from ... I decided on this based on a
> discussion I had with a person from DE Shaw's group a couple of years
> ago and he was referring to their folding simulations and reached the
> conclusion that this was the best combination in their hands until
> now. He also argued that the ILDN modifications alone (without the
> NMR-based modifications perform good enough, however with a little
> understabilization of helical conformations).
>
> From my personal experience, I cannot tell you how this combination
> works on very long time scale since my longest simulations are about
> 100 ns ...
>
> The force field evaluation studies by D.E. Shaw et co. have been
> published in by Lindorff et al in 2012 in PloS One.
>
> Hope this helps
>
> Best
> Vlad
>
>
>
> On 11/21/2012 02:56 PM, Albert wrote:
>> Hi Vlad:
>>
>> thanks a lot for kind comments.
>> Yes, probably I emphasize too much on CHARMM FF. Of course, they
>> also
>> use Amber FF. ;-)
>>
>> If I interpret well for your statements that: it is better to take
>> the either amber99ILDN or the modified CHARMM FF for long time scaled
>> MD.
>>
>> best
>> Albert
>>
>>
>> On 11/21/2012 02:50 PM, Vlad Cojocaru wrote:
>>> Dear Albert,
>>>
>>> I believe you are mistaken here. D.E. Shaw et co. have been using
>>> own-modified versions of both AMBER and CHARMM in their long
>>> simulations. In one talk from his group it was argued that their
>>> modifications of these 2 ff work well for the cases they investigated.
>>> In all talks I have seen from his group their modifications (e.g. ILDN
>>> modifications in AMBER) performed better on long(er) time scale than
>>> the
>>> original counterparts (e.g. ff19SB-ILDN versus original ff99SB, same
>>> holds true for CHARMM)...
>>>
>>> Best,
>>> 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 - 06:30:04 PST
