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 - 06:30:03 PST
