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.w...@gmail.com
<mailto:mdaily.w...@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 <sp...@xray.bmc.uu.se
<mailto:sp...@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>.
sp...@xray.bmc.uu.se <mailto:sp...@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: tev...@bioacademy.gr <mailto:tev...@bioacademy.gr>
teva...@gmail.com <mailto:teva...@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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