From: George Patargias (gpat_at_bioacademy.gr)
Date: Fri Jun 07 2013 - 09:43:45 CDT
Hi Jerome
Many thanks for these comments.
Best
George
> Hi George,
>
> ----- Original Message -----
>> Hello
>>
>> I would like to set up an ABF simulation to study the conformational
>> change
>> of a protein using as a colvar the C-alpha RMSD of two conformational
>> states.
>>
>> What is the reason of defining the
>> lowerwallconstant/upperwallconstant
>> options;
>
> Typically with a RMSD, you will only need the upperWallConstant, as the
> natural tendency is to drift away from the
>
>
>> I am not sure I understand the meaning of the hideJacobian option. Is
>> it to be switched on or off?
>
> In doubt, leave it at its default value (no).
>
>> How can I decide on the value of the option fullSamples? By checking
>> the
>> PMF convergence?
>
> FullSamples affects the early stages of the simulation. Once you're
> looking at convergence of the PMF, it's a bit late to decide on it. The
> choice is a trade-off between the speed of the initial exploration, and
> non-equilibrium work in that period. In doubt, leave it at its default
> value.
>
>> Is there anything else to check for this particular colvar?
>
> Be aware that you won't see a value or zero, or very small values, and
> that the PMF will rise steeply for values close to zero. That's just a
> mathematical property of the RMSD function. To make sure to avoid
> numerical problems due to this singularity, you could set the
> lowerBoundary to a small but non-zero number.
>
> Cheers,
> Jerome
>
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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