[gmx-users] GROMOS carbohydrate forcefield 45a4

Neha Gandhi n.gandhiau at gmail.com
Wed Apr 1 14:24:27 CEST 2009

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.

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?

Your help is appreciated.
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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