[gmx-users] pull code

[Attilio]

Hi

Kay Gottschalk wrote:

> The profiles you get with pulling simulations are of an irreversible  
> (out-of-equilibrium) process. Thus, dissipation has a strong  
> contribution, and the forces/energies are higher than for the  
> equilibrium process. Furthermore, the reaction coordinate is biased  
> due to the choice of the vector you are pulling along - the 'best'  
> reaction coordinate for your process can be different, so that again  
> you may end up calculating higher forces. Therefore, it might well be  
> that the backward process happens spontaneously after 10 ns, even if  
> you calculate the high barrier for the forward process. Did you check  
> whether the forward process also happens spontaneously after a while?
> Cheers,
> Kay.

I simulated a total of ~21 ns, and the molecule does not seems 
intentioned to go back: associate to this process in fact there is a 
relaxation of structural DNA parameters towards those of DNA alone in 
solution, and also the interaction is strongest, so I don't think that 
the molecule can go back in the same time...

Cheers,
Attilio

>
>
> On Jun 23, 2005, at 6:35 PM, 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)
>> 2) I selected as a reference group a piece of DNA, and as a pulling
>> group the small molecule.
>>
>> 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, 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.
>>
>> Thanks,
>> Attilio
>>
>>
>> -- 
>> Attilio Vittorio Vargiu
>> PhD Student at SISSA/ISAS
>> via Beirut 4
>> I-34014 Trieste, Italy
>> tel +390403787335   fax +390403787528
>>
>>
>>
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-- 
Attilio Vittorio Vargiu
PhD Student at SISSA/ISAS
via Beirut 4
I-34014 Trieste, Italy
tel +390403787335   fax +390403787528