[gmx-users] Where will the problem be?

[qiwenpeng at sinap.ac.cn]

----- 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 10:14 PM
Subject: Re: [gmx-users] Where will the problem be?


> 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.

we both use relative length. the length /original length

so there is mistake in angstrom and nm

Thank you very much !!
> 
>> 
>> 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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>>>>
>>>>
>>>>------------------------------------------------------------------------
>>>>
>>>>_______________________________________________
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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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>>>
>>>------------------------------------------------------------------------
>>>
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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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