[gmx-users] Re: Re: Re: Glucose Ring transition

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 31 02:51:01 CET 2005

On Mon, 2005-01-31 at 10:35 +0530, Patel Ronak Y wrote:
> Dear Dr Spoel,
> I used nrexcl=3. I think it should be correct. I tried eleminating some of
> the intramolecular interactions of glucose ring but the problem persists.
> Once againg I would like to mention is that for galactose and N-acetyl
> galactosamine, the chair coformation is nicely maintained. In galactose
> hydroxyl group at C4 is axial and for glucose it is equatorial,
> configuration of all other carbons is same.
> Out of six torsions of glucose ring three are absolutely fine but other
> three are skewed up.
Obviously the correct conformation is still subject to large forces. Try
to find out where they come from by doing an energy minimization and
look at the individual energy terms. It is easy to define impropers
incorrectly, but ther could also be a pair interaction that should be
turned off.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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