[gmx-users] Can gromacs got average position of a molecule

[David van der Spoel]

qiwenpeng at sinap.ac.cn wrote:
> Dear All:
>  
> I use gromacs3.3 to simulate a DNA. After Equilibration I got the energy 
> of bond is about 240 kj/mol , but the status on an article is 130 kj/mol .
>  
> I think it may be the conformation of the molecule need to be average 
> over a few ps .
please be more specific. could be due to timestep.

>  
> Is there any functions that gromacs has enclude to do this?
>  
> Thank you all!!
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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