[gmx-users] Gromacs and tranport coefficients

[Lianqing Zheng]

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...)
http://journal.kcsnet.or.kr/publi/bul/bu03n2/178.pdf

>
>How does one compute thermal conductivity?
Similar to viscosity, one may integrate heat flow acf to get thermal
conductivity (see Dysthe, JCP 110:4047).

>> 
>> Lianqing
>> 
>> 
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>-- 
>David.
>________________________________________________________________________
>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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