Re: PME with Implicit solvent - Reg

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon May 20 2019 - 13:55:21 CDT

I would suggest reading the relevant portions of the user guide. There is
extensive description of the GB model implemented in NAMD. You might also
consider consulting the available literature.

NAMD is predominantly designed for all-atom explicit solvent simulations
and this is generally the gold standard for modeling solvation effects
(this is not to disparage the utility and accuracy of implicit models).

On Mon, May 20, 2019 at 1:59 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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