[gmx-users] Where will the problem be?

[David van der Spoel]

qiwenpeng at sinap.ac.cn wrote:
> ----- 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 9:44 PM
> Subject: Re: [gmx-users] Where will the problem be?
> 
> 
> 
>>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.?
> 
> 
> The DNA has 12 base pairs, it is about 2.5nm 2.5 nm 4 nm. After em I heat the system to 300k with DNA molecule fixed, then em second times, then heat to 300 k again and without any restraints.   After this,  I equilibrate the system for 500 ps. Then I use the output gro to stretch.
> 
> There is something wrong? or some other things?

I am not an expert on this kind of application, but I meant to ask 
whether you have integrated the force curve and compared to literature, 
and whether the literature ref used angstrom when you get nm.

> 
> thank you!!
> 
> 
>>>----- 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
>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>_______________________________________________
>>>>gmx-users mailing list
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>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>>_______________________________________________
>>>gmx-users mailing list
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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
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>_______________________________________________
>>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 
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>>
>>
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++