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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Received on Fri Apr 21 2017 - 06:30:03 PDT
