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From: BJÖRN KARLSSON <BJORN.KARLSSON.hik.se>

Date: Wed, 6 Jun 2007 09:56:05 +0200

Hi Amber Users!

I am actually having two questions:

I'm currently using the ptraj module in amber to generate radial distribution functions g(r) for different atom pairs of small organic structures in chloroform (with 20 of molecule A and 100 of molecule B).

I understand that in a homogeneous solution of let say pure water, an ordered structure of the molecules at certain intermolecular atom distances (e.g. O-O or O-H) will generate g(r) values greater than 1 and that g(r) will approximate 1 as the structure of the solvent approximates bulk density (from which the number density can be calculated).

Now to my first question. Since g(r) is the ratio between the actual number density of the studied atom divided by the number density expected from the bulk density, I guess my g(r) values will be totally wrong since the bulk density represents the mixture of all components and not just the pure substance (of the atom of interest). Have I totally misunderstood this? If not, is there I way to come around this problem?

My second question. I have read about the potential of mean force, PMF which can be calculated from the g(r) values according to w(r)=-kTlng(r) where w(r) is the PMF, k is the bolzmann constant and g(r) is the probability of finding a certain atom around another atom at a certain distance, r. Is it appropriate to use this relationship between g(r) and w(r) for the estimation of interaction energies between small organic molecules in non-polar solvents?

Thanks on advance

/Björn

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Received on Sun Jun 10 2007 - 06:07:06 PDT

Date: Wed, 6 Jun 2007 09:56:05 +0200

Hi Amber Users!

I am actually having two questions:

I'm currently using the ptraj module in amber to generate radial distribution functions g(r) for different atom pairs of small organic structures in chloroform (with 20 of molecule A and 100 of molecule B).

I understand that in a homogeneous solution of let say pure water, an ordered structure of the molecules at certain intermolecular atom distances (e.g. O-O or O-H) will generate g(r) values greater than 1 and that g(r) will approximate 1 as the structure of the solvent approximates bulk density (from which the number density can be calculated).

Now to my first question. Since g(r) is the ratio between the actual number density of the studied atom divided by the number density expected from the bulk density, I guess my g(r) values will be totally wrong since the bulk density represents the mixture of all components and not just the pure substance (of the atom of interest). Have I totally misunderstood this? If not, is there I way to come around this problem?

My second question. I have read about the potential of mean force, PMF which can be calculated from the g(r) values according to w(r)=-kTlng(r) where w(r) is the PMF, k is the bolzmann constant and g(r) is the probability of finding a certain atom around another atom at a certain distance, r. Is it appropriate to use this relationship between g(r) and w(r) for the estimation of interaction energies between small organic molecules in non-polar solvents?

Thanks on advance

/Björn

-----------------------------------------------------------------------

The AMBER Mail Reflector

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Received on Sun Jun 10 2007 - 06:07:06 PDT

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