[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 
> simulations?

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,
> Regards,
> 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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