[gmx-users] sugar chain

DV diegovallejo at mdq.com.ar
Fri Jun 27 23:13:00 CEST 2003

I've had the same problem with Argon (LJ) without water at 600 K, very low
density. The factor was 5 in that case.

Diego Vallejo
Instituto de Física de Líquidos y Sistemas Biológicos.
vallejo at iflysib.unlp.edu.ar

-----Mensaje original-----
De: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]En
nombre de Kay Gottschalk
Enviado el: Viernes, 27 de Junio de 2003 05:43 p.m.
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] sugar chain

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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