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. -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
