[gmx-users] sugar chain

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Fri Jun 27 22:42:01 CEST 2003

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 
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 

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