[gmx-users] oplsaa vs. charmm

[Da-Wei Li]

I really don't think you can get adequate sampling for IDPs that have 40
residues, using full atomic MD.


On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily <mdaily.work at gmail.com> wrote:

>  Do you have some experimental data to compare to your IDP simulations,
> like X-ray scattering or some such? I'd imagine that IDP simulations with
> either forcefield would only be qualitatively accurate given that the
> forcefields are calibrated, as you say, on rigid proteins and small
> molecules.
>
> On 6/8/11 8:00 AM, Thomas Evangelidis wrote:
>
> Dear Prof van der Spoel and GROMACS users,
>
> I have read the article "Scrutinizing Molecular Mechanics Force Fields..."
> where it is demonstrated that AMBER99sb yields protein conformations that
> are in better agreement with residual dipolar coupling, J-coupling and NOE
> data, compared with other force fields. However, both proteins used for this
> benchmark study (ubiquitin and protein G) are rather rigid, so I was
> wondering if there is a similar analysis for flexible proteins/peptides. I
> want to simulate a few intrinsically disordered proteins/peptides of length
> between 40 and 100 aa and would like to know what would be the best choice
> of force field to use. Any experience or knowledge on this matter would be
> greatly appreciated!
>
> thanks in advance,
> Thomas
>
>
>
> On 27 May 2011 19:01, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
>>  On 2011-05-27 17.50, simon sham wrote:
>>
>>> Hi,
>>> I have recently done two simulations on a protein at high temperature
>>> near its melting temperature. At the beginning I used CHARMM forcefield,
>>> and then OPLSAA to double check the results. There are some differences
>>> in the structures between the forcefield used. I know different
>>> forcefields can give different results. All parameters in the
>>> simulations were the same except the forcefield. Is there anyway I can
>>> tell which forcefield gives more reliable results?
>>>
>>> Thanks for the insights,
>>>
>>> Simon
>>>
>>>   You might want to check
>>
>> Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing
>> Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data
>> Biophys. J. 99 pp. 647-655 (2010)
>>
>> where we compare a number of FFs to NMR data.
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>
>> --
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>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang at bioacademy.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
>
> --
> Michael D. Daily, Ph.D.
> Postdoctoral Fellow
> Qiang Cui group
> Department of Chemistry
> University of Wisconsin-Madison
>
>
> --
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