Neha Gandhi wrote:
Dear List,
In the paper entitled "A new GROMOS force field for hexopyranose-based
carbohydrates" Journal of Computational Chemistry Volume 26 Issue 13,
Pages 1400 - 1412. When the authors ran unrestrained md for 2ns, once
the conformation is stabilised in chair, they donot observe any
further transitions.
Another paper describes the inversions of the pyranose ring within a
1-ns MD simulation at 600 K. I m running NPT simulations at 310 as
well as 400 K of sulfated pyranose rings using GROMOS ff in gromacs. I
start my simulation with boat conformation which intercoverts to chair
within 60 ps but I cannot see the transitions back and forth.
Of,course I see transitions back and forth when i increase the
temperature to 800K.
Based on what you have described as being published already, none of this should
be surprising. At lower temperature, you do not observe the transition, but at
higher temperature you do. Think about optimal geometry for a sugar. The boat
form is disfavored relative to the chair form, especially when you start adding
bulky substituents. Do the published works discuss large substituents? If they
do not, you cannot expect to draw direct conclusions about your own work.
Also realize that 60 ps is an extremely short timeframe to expect such
interconversions, especially since the other studies you cite ran at least 1 ns
or more.
Did any body try to simulate such sugars where they observe
boat->chair->boat transitions using GROMOS? How long did it took? Was
it at room temperature? What parameters are important to validate ff
for such molecules?
You've got the primary literature for the parameter sets, so you should know how
the authors went about validation.
-Justin
Your help is appreciated.
--
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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