[gmx-users] Where will the problem be?

[David van der Spoel]

qiwenpeng at sinap.ac.cn wrote:
> Hello everyone:
>  
> I stretched a DNA molecule, and get a graph of extension vs. force. My 
> result is very like the graph in several articles in shape. But the 
> number of my force is about five times larger than the number in the 
> articles.
>  
> Where will the problem be?
>  
> There is something wrong in the pdb file? my mdp file isn't 
> right? my protocl isn't suitable? or there is something else? 

Have you tried to reproduce exactly a literature example?
How about the speed of pulling? Is that comparable?


> 
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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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