[gmx-users] oplsaa vs. charmm

[Justin A. Lemkul]

Da-Wei Li wrote:
> I really don't think you can get adequate sampling for IDPs that have 40 
> residues, using full atomic MD.
> 

I disagree.  Perhaps brute force MD would not accomplish the task (unless you 
have considerable resources and don't want your answers very quickly, but even 
then...), but there are certainly a number of techniques, including implicit 
solvent, REMD, generalized Hamiltonian replica exchange, and fancy umbrella 
sampling and/or free energy settings that can vastly improve sampling for such 
systems.

-Justin

> 
> On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily <mdaily.work at gmail.com 
> <mailto: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
>>     <mailto: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
>>         <tel:%2B46184714205>.
>>         spoel at xray.bmc.uu.se <mailto: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 <mailto:tevang at bioacademy.gr>
>>
>>               tevang3 at gmail.com <mailto: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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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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