[gmx-users] sugar chain

[David]

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. 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++