[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 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?

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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
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