## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_cmm.chem.upenn.edu*)

**Date:** Mon Aug 25 2008 - 15:14:35 CDT

**Next message:**Axel Kohlmeyer: "Re: resid of water that is hydrogen bonded"**Previous message:**Axel Kohlmeyer: "Re: Failure to open PDB files"**In reply to:**Maxim Paliy: "measure gofr - how is g(r) normalised?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Mon, 25 Aug 2008, Maxim Paliy wrote:

MP> Hi All

hi maxim,

MP> I've a couple of quick questions about "measure gofr" command

MP>

MP> 1) how exactly the unnormalised histogram (last output list) is

MP> normalised to the second output list?

MP> i.e. what is the density rho ?

is the "pair-particle" density formed by both selections averaged

over either the volume of the simulation cell - in case of pbc aware

calculations - or else assuming the particle density of water (without

PBC the density is not a well defined entity anyways). this density

excludes "self-pairing". the resulting graph does not need to

be corrected for finite size effects, i.e. it approaches 1.0 instead

of (n-1)/n in the case of n particles of the same type.

MP> 2) In the manuals, the factor 4pi seems to be missing from the formula

MP> for the third output list

MP> (runnig coordination number n(r) = int( rho*g(r)*r^2*dr ).. Is this a

MP> typo in the manuals?

well, as it is scaling factor one could claim it is included

in "rho". in any case, the integral is computed directly from

taking the sum over the averaged histogram bins, like in:

n(r) = Sum_i=0..k <h(i)>, with k = r/delta (delta=bin width).

as this is the only way to correctly compute this value from

simulations where the number of particles in the selections

changes over time.

in case you observed any (minor?) inconsistencies, please note

that a couple of bugs that were mostly (but not completely)

compensating each other have been found and fixed recently in

the measure gofr code and that the vmd alpha releases are commended

to use for any application that depends on accurate numerical results.

cheers,

axel.

MP>

MP> thank you advance for clarifications,

MP> Maxim

MP>

-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.

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