Re: PME with Implicit solvent - Reg

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon May 20 2019 - 17:03:04 CDT

Dear Manikandan,

The generalized Born implicit solvent represents ions in the solution
implicitly. As far as I know, it's not designed to be used with
explicit ions. I think an explicit solvent representation is best for
what you are doing. To do what you are suggesting would probably
require development of a new method, implementation and validation.

Regards,
Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Mon, May 20, 2019 at 1:00 PM Mani Kandan <manikandand5110_at_gmail.com> wrote:
>
> Thanks. I am studying effect of the solvent on the ion transport through nanopore. For that purpose, I need to add effect of the solvent i.e water implicitly to the system containing pore and ions. How can I do that and is it possible to get effect of the solvent using implicit solvent model in namd?
>
> I need an help in this regard. And is any other way to do?
>
>
> With regards
>
> Manikandan
>
> On Mon, May 20, 2019, 11:21 PM Brian Radak <brian.radak_at_gmail.com> wrote:
>>
>> When in doubt, try it, although that's not to say that all combinations of keyword options are recommendable from a scientific perspective.
>>
>> Based on a quick read of the source code you should receive the very clear exit message "GBIS not compatible with PME"
>>
>> HTH,
>> BKR
>>
>> On Mon, May 20, 2019 at 10:10 AM Mani Kandan <manikandand5110_at_gmail.com> wrote:
>>>
>>> Hello all,
>>>
>>> Is PME compatible with implicit solvent? I want to apply the electrostatic interaction effect of water through implicit solvent method and in meanwhile, have to calculate the electrostatic interactions between other atoms through PME. Is this case possible?
>>>
>>> Kindly let me know.
>>>
>>> Regards
>>> MANIKANDAN D

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