[gmx-users] course grain model for DNA

[Justin A. Lemkul]

He, Yang wrote:
> Hi Justin,
> 
> Thank you for your reply. In fact , for this base pair of "Gb2  Cb2  1          0.000194e10   0.00217e4",  whatever I do , the final result for this base pair is the same they will always separate from each other. Hence, I doubt whether this is because gromacs did not read my force field file at all.
> 
> I hope to get your further suggestions about that.
> 

What magnitude of values have you tried?  Using 0.000194e10 (1.94e7) for epsilon 
seems huge, but then, the only CG force field I've ever used is MARTINI (and 
only with only a little experience).  The magnitudes of sigma and epsilon for 
that force field are on the order of e0, e-01, etc.

How are you determining your sigma and epsilon values?

-Justin

> Thank you .
> 
> Yang
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, November 25, 2008 3:06 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] course grain model for DNA
> 
> He, Yang 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.
>>
> 
> Well, that line is commented out (;), so naturally it would have no effect.
> 
> -Justin
> 
>> So ,I got confused about this phenomenon . Can anyone of you give me some suggestions?
>>
>> Thank you in advance.
>>
>> Yang
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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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-- 
========================================

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

========================================