[gmx-users] Re: Thanks!
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 11 02:58:26 CEST 2006
Steven Kirk wrote:
> Ok yes, they use the trick of giving the shell a mass of 0.4 amu and
> reducing the standard oxygen mass by the same amount.
> When I solvate my macromolecule with the equilibrated water model,
> however, I get convergence to machine precision with large (E+06) forces
> in the EM stage, and PR and full MD runs start OK but after about 70 x
> 0.001ps mdrun_d throws lots of LINCS errors and segfaults. The problem
> doesn't just lie on one water molecule - I tried deleting the water
> molecule causing the problem, but there was just another one somewhere
> else to take its place.
> Have you seen any behaviour like this in any of your shell water
the problem is most likely due to incompatible force fields, for
instance because the hydrogen atoms do not carry a vanderwaals
interaction. you don't say what the nature of the macromolecule is or
the force field that you use. check what kind of interactions causes
this; the general solution would be to have a polarizable FF for the
macromolecule as well.
> Any advice gratefully received,
> Steve Kirk
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://folding.bmc.uu.se
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