AMBER Archive (2006)

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

From: j j (fantvamp_at_gmail.com)
Date: Mon Dec 04 2006 - 06:56:54 CST

Everything works fine now.
I've recompiled ptraj aplying this latter modification and got the
_carnal.xmgr.
Thank you very much.
JJ

2006/12/1, Thomas Cheatham <tec3_at_utah.edu>:
>
>
> > 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:
>
> histogram[bin]
> ----------------------------------------------------------
> (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.
>
> --tom
>
>
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