From: Walter Rocchia (Walter.Rocchia_at_iit.it)
Date: Thu May 26 2011 - 06:02:03 CDT

Hi Marek,

It should be possible, to use the DelPhi PB solver and to get the electrostatic potential over a set of dots lying on the molecular surface, obtained with a given probe radius.
You could do this over a set of snapshots coming from an MD trajectory and you should also be able to connect each dot to the closest surface atom.

Keep in mind that during a trajectory some atoms might be sometimes buried and sometimes exposed, so that the superficial electrostatic potential could be undefined in some snapshots.

Best
Walter

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of Marek Maly
> Sent: Thursday, May 26, 2011 11:29
> To: Axel Kohlmeyer
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Mean value of el. potential ?
>
> Hello Axel,
>
> thanks a lot for your prompt answer !
>
> I think, that suggested characteristic (mean value of surface
> potential)
> might
> converge. Of course one should use enough frames from the trajectory,
> so
> for
> the particular molecule not calculate this property just from one frame
> as
> such value
> has small representative meaning especially in case of more flexible
> molecules.
> Moreover if one do this "measuremet" not directly on vdw surface or
> water
> accessible surface,
> but on surface accessible to "bigger probe" (let say three, four times
> bigger then usual H2O probe (1.4A)),
> the convergence properties should be improved. The idea of this
> characteristic came from
> need to have some quantitative characteristic which might be correlated
> with
> experimental zeta potential measurements when comparing several
> differently charged molecules thats all...
>
> Anyway thanks again for your comments and of course I would be grateful
> to
> anybody for
> another suggestions regarding some quantitative characteristic which
> might
> be correlated with zeta potential
> results.
>
> Best wishes,
>
> Marek
>
>
>
>
>
> Dne Thu, 26 May 2011 02:51:55 +0200 Axel Kohlmeyer <akohlmey_at_gmail.com>
> napsal/-a:
>
> > 2011/5/25 Marek Maly <marek.maly_at_ujep.cz>:
> >> Hello all,
> >>
> >> with "APBS Electrostatics" VMD plugin is possible to calculate
> >> electrostatic
> >> potential around given molecule. Molecular surface might be colored
> >> according
> >> to potential values but is there any possibility for calculation of
> mean
> >> value of
> >> electrostatic potential on molecular surface (so simply the
> potential
> >> average over all grid points
> >> which represent molecular surface ) in VMD ?
> >
> > no.
> >
> >>
> >> If not, is there any other SW which could do this job if one provide
> >> molecular structure
> >> (e.g. *.pdb file) and potential values (i.e. *.dx file) calculated
> >> previously using "APBS Electrostatics" VMD plugin ?
> >
> > none that i know if. it is a pretty ill-defined property,
> > since "molecular surface" is rather arbitrary.
> > if anything, the integral over a volume is probably more
> > meaningful, as it would hopefully converge to something
> > with decreasing density isosurface cutoff.
> >
> > but then again, you have to be careful to normalize this
> > correctly, especially for charged molecules.
> >
> > cheers,
> > axel.
> >
> >> Thanks a lot in advance for any useful comments !
> >>
> >> Best wishes,
> >>
> >> Marek
> >>
> >
> >
> >
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/