[gmx-users] course grain model for DNA

[Justin A. Lemkul]

He, Yang wrote:
> Hi Mrinalini.
> 
> Thank you for your suggestions. In my previous case, I never use the distance restraints . So I wonder whether you can provide me a sample for file of the disres.itp .In fact, I don't know much about this file' form and how to set values in the file.
> 

Manual section 4.3.4; it doesn't have to be a separate .itp file if you don't 
want.  You can just add a [ distance_restraints ] section in your system topology.

-Justin

> Thank you.
> 
> Yang
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mrinalini Puranik [mrinalinip at gmail.com]
> Sent: Tuesday, November 25, 2008 3:59 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] course grain model for DNA
> 
> If there is fraying at the edges only, you can impose distance
> restraints on some of the hydrogen bonds at the ends. You need to
> modify md.mdp to turn on distance restraints and have a new file
> called disres.itp that mentions the distances to be restrained.
> 
> Hope this helps,
> Mrinalini
> 
> 
> On Wed, Nov 26, 2008 at 1:06 AM, He, Yang <yang.he at mavs.uta.edu> wrote:
>> Hi all users,
>>
>> when I am using the gromacs to simulate the course grain model for DNA, it seems that the software doesn't recognize my force field file. I have included all the bond and non-bond parameters in the bon.itp and nb.itp file.
>>
>> During my simulation , I found that the base pair for C-G which first are in the balance distance always repel from each other so I try to increase the value of epsilon to increase the dispersion between this pair but it still did not work and the pair still  repelled  from each other after the simulation .
>>
>> Then I tried like this "   ;  Gb2  Cb2  1          0.000194e10   0.00217e4 " in my nb.itp file,  I found that the simulation can still be carried on and the simulation result is the same for this base pair.
>>
>> So ,I got confused about this phenomenon . Can anyone of you give me some suggestions?
>>
>> Thank you in advance.
>>
>> Yang
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> 
> 
> 
> --
> Mrinalini Puranik
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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