Thanks a lot..
Lorenzo
Il giorno 18/feb/09, alle ore 18:15, Thomas Cheatham III ha scritto:
>
>> I obtained a couple of AMBER trajectories and I calculated the RDF
>> with ptraj, and then calculated the structure factor by Fourier
>> transformation with a in-house code.
>> The fit with experimental data is very good at intramolecular
>> distances (high k values), but gets worser at high distance..I guess
>> that there could be some problems with the finite-size effects, since
>> ptraj RDF are (obviously..) calculated within the hypothesis of
>> minimum image convention, so that the maximum r value is half the box
>> dimension.
>> Does any body have suggestions on how to estimate the g(r) outside
>> the box and/or suggest me some papers on this issue?
>
> The ptraj code could be modified to include the longer range g(r)
> information, however it is not clear if this would be that useful
> since it
> would likely be biased by finite-size effects (essentially,
> continuously
> running into copies of the solute in an ordered array rather than
> random
> distribution).
>
> Two thing's I would try:
>
> (1) run with a bigger box
>
> (2) extrapolate the RDF to unity (1.0) from 1/2 the box size on...
> This
> will effectively omit the long range components but not be biased
> by the
> artificial drop of g(r) as you approach sizes greater than 1/2 the box
> size due to the minimum image.
>
> --tec3
>
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Received on Fri Feb 20 2009 - 01:15:12 PST
