AMBER Archive (2009)

Subject: Re: [AMBER] g(r) extrapolation

From: Lorenzo Gontrani (
Date: Thu Feb 19 2009 - 03:23:19 CST

Thanks a lot..

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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