[gmx-users] Where will the problem be?

[David van der Spoel]

qiwenpeng at sinap.ac.cn wrote:
> 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

How about number of base pairs, angstrom vs. nm etc.?

> ----- 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?
>>
>>
>>
>>>
>>>------------------------------------------------------------------------
>>>
>>>_______________________________________________
>>>gmx-users mailing list
>>>gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please don't post (un)subscribe requests to the list. Use the 
>>>www interface or send it to gmx-users-request at gromacs.org.
>>
>>
>>-- 
>>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
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.
> 
>>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++