[gmx-users] Polymers: Shake Problem

[David van der Spoel]

acorrea at unisa.it wrote:
> Dear all,
> I am trying to simulate a polymer, with high molecular mass, on parallel 
> machines.
> If I try to compile with a number of cpu = or > 4 I found this problem:
> 
> ?Shake block crossing node boundaries?
> 
> I know?..I have constraints between atoms crossing node boundaries but 
> this came from the polymer structure.
> 
> Someone knows how I could solve this problem?
> 
> Thank you and
> happy new year
> 
> Andrea
> 
> 
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Currently your only option is to restrict constraints to h-bonds only.
You should then reduce your time step to 1 fs.
-- 
David.
________________________________________________________________________
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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