[gmx-users] Where will the problem be?

[qiwenpeng at sinap.ac.cn]

They use different  DNAs and the result is almost same.

So I use the dickerson DNA and ffamber 94/99, All of them  in the http://folding.stanford.edu/ffamber. the speed is very same the one in the article.

Can you give me some advices
----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, December 22, 2005 8:51 PM
Subject: Re: [gmx-users] Where will the problem be?


> 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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