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
On 11/21/2012 02:37 PM, Albert wrote:
> Yes, as we read the long time scaled MD paper from Deshaw group, they
> prefer CHARMM27 FF. If we read the methods and materials,which probably
> most people forget to care about, we always find the following sentence:
>
> /All simulations used the CHARMM27 force field for protein, ions, and
> water (51, 52); the//
> //CHARMM36 force field was used for lipids (53). Torsional backbone
> corrections: U = k·Σm//
> //(−1)m−1 · [(1 + cos m(φ − φ'))/m!], (m = 6 and k = 9.2 kcal·mol−1),
> centered at φ' = φxtal − 180°;//
> //were applied to SF residues Gly376 and Gly378 to prevent SF
> degradation on a timescale of//
> //microseconds (21); φxtal ~ 50° and φxtal ~ 100° for these residues in
> the crystal structure (10)./
>
> here is full text for it, in page 2 you can find those statements.
>
> That's why I asked if nowadays Amber FF good enough for such kind of
> purposes.
>
> best
> Albert
>
>
>
> On 11/21/2012 01:37 PM, David A Case wrote:
>> On Wed, Nov 21, 2012, Albert wrote:
>>>> I've got a question for the Amber99-ILDN and recent Amber12SB FF. Are
>>>> they good enough for long time scaled MD simulation such as tens of
>>>> microsecond ?
>> The answer must depend on the type of system (protein?) you are planinng
>> to simulate, and how you define "good enough". The DEShaw group has
>> reported long simulations with the ILDN modifications to Amber99SB, and
>> the modifications involved in ff12SB are of a similar nature. My group
>> has done a number of 1-2 microsecond simulations of very stable proteins
>> that show good structural equilibration and no long-term drift, using
>> ff12SB. But the generic question you proposed is surely unanswerable.
>>
>> ....dac
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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 - 06:00:06 PST
