Dear Jim
Thank you for your reply. The diameter is in nm scale. The process is
Electrospray process and I was hoping to be able to change the dielectric
constant during the simulation for the present water molecules by dielc
parameter in mdin and having an igb of 6 to have vacuum run in pmemd. But I
don't know if changing dielc is going to effect the dielectric constant of
my droplet. What I got from David, it seems impossible.
On Friday, April 21, 2017, James Kress <jimkress_58.kressworks.org> wrote:
> Perhaps you should explain the experiment you performed and its results to
> see if the simulation you are trying to perform corresponds to the
> experiment.
>
> I have a hard time believing that a 3 angstrom diameter drop of H2O has a
> dielectric constant that differs significantly from 1.
>
> Jim Kress
>
>
> -----Original Message-----
> From: Samaneh Ghassabi Kondalaji [mailto:saghassabikondalaji.mix.wvu.edu]
> Sent: Friday, April 21, 2017 9:36 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Internal dielectric constant and pmemd
>
> Unfortunately the process I am simulating says otherwise from experimental
> point of view. I determined the values and now I need to apply them to my
> system.
>
> On Fri, Apr 21, 2017 at 9:26 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Sam:
>>
>> you said that:
>>
>> "I need to change the dielectric constant of water in this droplet
>> from 78.5 to 1 and at the same time preserve the vacuum."
>>
>> And what I am telling you is that the dielectric constant of your
>> system is already equal to 1 for the water, so I do not understand
>> what your issue is.
>> There is nothing to change from 78.5 to 1, it is already 1.
>>
>> adrian
>>
>>
>> On 4/21/17 9:21 AM, Samaneh Ghassabi Kondalaji wrote:
>> > I understand what igb=6 does to my system in terms of
>> > dielectric constant and I actually need the value of one as I am in
>> > vacuum, but Is there ANY way in pmemd that I can have two different
>> > dielectric
>> constants (
>> > it seems unrealistic but it is what it has to be!).
>> > Cheers,
>> > Sam
>> >
>> > On Fri, Apr 21, 2017 at 9:14 AM, Adrian Roitberg <roitberg.ufl.edu>
>> wrote:
>> >
>> >> The dielectric constant of your system will be ONE without you
>> >> doing anything.
>> >>
>> >> The fact that you are using igb=6 immediately does that, and the
>> >> fact that you have water molecules does not make any difference.
>> >>
>> >> adrian
>> >>
>> >>
>> >> On 4/21/17 9:11 AM, Samaneh Ghassabi Kondalaji wrote:
>> >>> Yes, it seems very confusing but my system is a peptide in a
>> large
>> >>> water droplet (~3.0 nm in diameter) present in vacuum and I need
>> >>> the
>> >> water
>> >>> molecules to leave the system gradually. I use igb=6 so I can use
>> >>> pmemd
>> >> for
>> >>> vacuum simulations. I need to change the dielectric constant of
>> >>> water
>> in
>> >>> this droplet from 78.5 to 1 and at the same time preserve the vacuum.
>> >> Can I
>> >>> just do it with dielec or I will need external, internal
>> >>> dielectric parameters?
>> >>> Best
>> >>> Sam
>> >>>
>> >>> On Fri, Apr 21, 2017 at 8:04 AM, David Case
>> >>> <david.case.rutgers.edu>
>> >> wrote:
>> >>>> On Thu, Apr 20, 2017, Samaneh Ghassabi Kondalaji wrote:
>> >>>>
>> >>>>> I am performing a simulation that requires the change of
>> internal
>> >>>>> dielectric constant and of course the non-default values of
>> >>>>> intdiel
>> are
>> >>>> not
>> >>>>> supported in pmemd. I was wondering if anyone has found a way
>> >>>>> around
>> >> it?
>> >>>>> Has there been a bugfix recently that fixes this? Is it possible
>> >>>>> to
>> use
>> >>>> the
>> >>>>> dielct value of matching the desired intdiel but use a different
>> >> extdiel
>> >>>> or
>> >>>>> the dielct parameter will override the extdiel? I am using pmemd
>> >>>>> and
>> >>>> igb=6
>> >>>>> to simulate a very large system in the gas phase and I am not
>> >>>>> going
>> to
>> >> be
>> >>>>> able to use sander for my purpose.
>> >>>> I am confused here: if you are using igb=6, the concepts of a
>> "internal"
>> >>>> and
>> >>>> "external" dielectric don't come into play. Any values you tried
>> >>>> to
>> >> enter
>> >>>> there would be ignored.
>> >>>>
>> >>>> ....dac
>> >>>>
>> >>>>
>> >>>> _______________________________________________
>> >>>> AMBER mailing list
>> >>>> AMBER.ambermd.org
>> >>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>
>> >>>
>> >> --
>> >> Dr. Adrian E. Roitberg
>> >> University of Florida Research Foundation Professor Department of
>> >> Chemistry University of Florida roitberg.ufl.edu
>> >> 352-392-6972
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>>
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor Department of
>> Chemistry University of Florida roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> *Samaneh ghassabi kondalaji*
> *PhD student in Chemistry*
> *555 CRL, Chemistry department*
> *West Virginia University *
> *Morgantown, USA*
>
> *E-mail: **saghassabikondalaji.mix.wvu.edu*
> <saghassabikondalaji.mix.wvu.edu>
> _______________________________________________
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> AMBER.ambermd.org
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>
>
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>
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Fri Apr 21 2017 - 11:30:02 PDT
