[gmx-users] sugar chain

David spoel at xray.bmc.uu.se
Fri Jun 27 22:46:01 CEST 2003

On Fri, 2003-06-27 at 22:42, Kay Gottschalk wrote:
> Hi there,
> when I calculate the diffusion coefficient with r_msd -mol of my 
> solvent (water), I get a coeffieint of ~ 4.7 10e-5 cm^2/s - that is 
> factor 2 too high. Is this a) a bug or b) a parameter error of SPC 
> water or c) am I doing it wrong? I do it over different 
It is correct. Depends a bit on coulomb treatment etc. SPC/E is better.

> time-intervalls, from 2 to 500 ps. and the result is consistent. As 
> -trestart doesn't work for me in combination with -mol, I just use the 
> default. But if I am not misstaken, -trestart doesn't really help 
> anyway - I don't think the statistics get any better. Thanks for  your 
> thoughts,
> Kay. 
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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