VMD-L Mailing List

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Thu May 26 2011 - 06:51:44 CDT

Hi Walter,
thanks a lot for your suggestion, I will check it ...

    Best wishes,

        Marek

Dne Thu, 26 May 2011 13:02:03 +0200 Walter Rocchia <Walter.Rocchia_at_iit.it>
napsal/-a:

> 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/
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 6154
> (20110526) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
> 

-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/