[gmx-users] pull code

[Jens Krüger]

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?

Best wishes,

Jens

>
>
> 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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