[gmx-users] Gromacs and tranport coefficients
lzheng at me.rochester.edu
Fri Nov 7 18:37:01 CET 2003
On 7 Nov 2003, David wrote:
>On Fri, 2003-11-07 at 17:34, Lianqing Zheng wrote:
>> Dear Gromacs pals:
>> I know Gromacs can calculate self-diffusion coefficient, how about
>> viscosity and thermal conductivity? Thanks.
>viscosity from energy file (pressure tensor) is very nosiy
>or from special simulations (see Hess, JCP 116 (2002) p. 209
>and Wensink, JCP 119 (2003) p. 7308).
Yeah, I also found that it takes long long time to converge. Here is an
article using "atomic" pressure tensor in acf to get a much faster
convergence. However I tried to repeat its results but couldn't (still
checking the code...)
>How does one compute thermal conductivity?
Similar to viscosity, one may integrate heat flow acf to get thermal
conductivity (see Dysthe, JCP 110:4047).
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>David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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