VMD-L Mailing List

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Thu May 26 2011 - 04:29:12 CDT

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
>>
>
>
> 

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