[gmx-users] Wheter the drift velocity has been removed from calculating the temperature?

[David van der Spoel]

Hu Zhongqiao wrote:
> 
> 
> Dear all,
> 
>  
> 
> I wonder if the drift velocity has been removed from calculating the 
> temperature for a non-equilibrium MD in which a directional movement for 
> a group exists due to external force applied.
> 
Yes it is. Please check the source code in src/mdlib/update.c

>  
> 
> One paper, entitled “Why are carbon nanotubes fast transporters of 
> water?” (Joseph and Aluru, Nano Letters, web release version in Feb. 
> 2008), mentioned that “the mean axial velocity of water was subtracted 
> from the axial component of the velocity of each water molecule as 
> implemented in ref 20.” Here the ref 20 is the one (Lindahl et al., 
> Gromacs 3.0: a package for molecular simulation and trajectory analysis. 
> J Mol Model, 2001, 7:306-317). Unfortunately I did not find such 
> information in ref 20.
> 
>  
> 
> Anyone can tell me the clear answer on this?
> 
>  
> 
> Thanks,
> 
> Zhongqiao
> 
>  
> 
> 
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> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se