[gmx-users] GROMOS carbohydrate forcefield 45a4

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 1 20:24:24 CEST 2009

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.


> 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


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