AMBER Archive (2006)

Subject: Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?

From: Thomas Cheatham (
Date: Fri Dec 01 2006 - 16:01:35 CST

> Thank you very much for your detailed reply, hbond for MG works fine now.
> Radial distribution gave me two outputs,
> rdf_phosphate_volume.xmgr and rdf_phosphate_standard.xmgr,
> should be also expected rdf_phosphate_carnal.xmgr?

In reply to this and the list, it is often a good idea when people have
trouble understanding my poor ptraj manual to look at the top of the
subroutines for the various "actions", i.e. in ptraj/actions.c
transformAction() where action corresponds to the command.

Regarding the three outputs to the radial command (calculating radial
distribution functions), originally ptraj output three files, that
corresponding to the definitions below where "histogram[bin]" is the count
at that particular distance bin, "R" is the distance and "delR" the
spacing between bins, "frames" is the total number of snapshots visited,
and "molecules" is the number of atoms being counted...

(1) *_standard.xmgr, i.e. the standard definition of a RDF, such as in
Allen & Tildesley:

   (4/3)*pi*density*[(R+delR)**3 - R**3] * frames * molecules

where density is assumed to be water at 1.0 (converted to appropriate
units, angstroms**3, leads to a value of 0.033456) or can be altered with
the "density <value>" keyword.

(2) *_volume.xmgr, i.e. one where instead of density, the volume of the
system is used:

              histogram[bin] * volume
     (4/3)*pi*[(R+delR)**3 - R**3] * frames * molecules

(3) *_carnal.xmgr, i.e. how carnal calculated it:

     histogram[bin] * (Rmax**3 - Rmin**3)
     [(R+delR)**3 - R**3] * measurements

This value does not tail appropriately to unit density and as carnal is
no longer supported, I disabled it in ptraj. Internally it is simply
wrapped with if ( 0 ) {} so could be trivially added back in locally if
desired to reproduce old data.

In general, if you've got a system in water, the *_standard.xmgr is an
appropriate choice.

Hope this helps.


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