[gmx-users] pull code

[Attilio]

Jens Krüger wrote:

>Hi Attilio,
>
>I have no experience with DNA simulations, but I used AFM to pull ions
>through membrane channels.
>
>Attilio wrote:
>
>  
>
>>Hi all,
>>
>>I have a questio concerning the feasibility of a steering dynamics on my
>>system. I want to push a small molecule along the minor groove of the
>>DNA, so:
>>
>>1) I removed all the constraints on bonds (no LINCS or SHAKE)
>>    
>>
>
>Why did you? In the 3.2 manual they say on page 119:
>
>• not possible currently: between groups of atoms that are part of a larger
>molecule for which the bonds are constrained with SHAKE or LINCS.
>
>So in your case: two seperate molecules => SHAKE or LINCS can be used.
>  
>
>  
>
>>2) I selected as a reference group a piece of DNA, and as a pulling
>>group the small molecule.
>>
>>    
>>
>
>Sounds good to me.
>
>  
>
>>Maybe I miss something of the warnings in the manual, but I didn't
>>understand if the profiles I get are reliable or not (I calculate works
>>of ~15 Kcal/mol,
>>    
>>
>
>I get maximum forces around 100 pN. So if I say Work = Force*Way, it gives
>energies around 50 kJ/mol or 12 kcal/mol. But I am not sure, how much
>"physical" sense these values make, if you compare them, for example, with
>binding energies.
>
>  
>
>>but the inverse process -i.e. the movement of the
>>molecule in the opposite of the pulling direction- happens spontaneously
>>after 10ns!), since I take a part of a molecule as reference group, but
>>also I removed all the constraints.
>>    
>>
>
>That is quite a long simulation time. Did you do multiple runs, to verify
>that it did not happend just by chance? Is the small molecule charged and
>what is with the electrostatics?
>  
>
Hi Jens,

Ok, I have two different simulations in which the movement of the little 
molecule along the DNA minor groove happens. In fact initially I was 
worried about the result, then I relaxed the structure of the drug (ab 
initio) with strongest conditions and I changed a little bit the 
parameters, but the movement happened about at the same time. In 
addition the molecule is not charged at all, and its electrostatic 
interaction with DNA is quite poor...

Cheers,
Attilio

>Best wishes,
>
>Jens
>
>  
>
>>Thanks,
>>Attilio
>>
>>--
>>Attilio Vittorio Vargiu
>>PhD Student at SISSA/ISAS
>>via Beirut 4
>>I-34014 Trieste, Italy
>>tel +390403787335   fax +390403787528
>>
>>_______________________________________________
>>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
>>www interface or send it to gmx-users-request at gromacs.org.
>>    
>>
>
>--
>========================================================
>Jens Krüger
>mercutio at uni-paderborn.de
>dienstlich:
>Warburger Str. 100 * 33098 Paderborn * Tel.:05251-602183
>privat:
>Ellersteg 3 * 33100 Paderborn-Dahl * Tel.:0176-20042288
>========================================================
>
>  
>


-- 
Attilio Vittorio Vargiu
PhD Student at SISSA/ISAS
via Beirut 4
I-34014 Trieste, Italy
tel +390403787335   fax +390403787528