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
>>>>
>>>>
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>>>
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
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>>
>
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Apr 21 2017 - 06:30:05 PDT
