[gmx-users] Implicit and Explicit solvation

[Syed Azeem]

Hi Justin,

Thank you so much for the info.
I'll perform the simulation with explicit solvent and calculate the free energy.

Azeem

> MM/PBSA is a post-processing (analysis) method in which you provide existing
>
> snapshots and the MM energy is combined with a PBSA estimate of solvation
> free
> energy to give the free energy of the system.  The (unofficial) g_mmpbsa
> tool
> does this.  It does not require additional simulations.
>
> -Justin
>
>>
>>> From: Timofey Tyugashev <tyugashev at niboch.nsc.ru>
>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>>> Subject: Re: [gmx-users] Implicit and Explicit solvation
>>> Message-ID: <17ce8acf-3566-f23f-3931-77ed00c37995 at niboch.nsc.ru>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>
>>> Implicit solvation treats solvent as a continuous medium (a kind of
>>> modifier for , while explicit one treats it as a set of explicit
>>> (surprise!) particles. I guess you can start reading from relevant
>>> Wikipedia articles.
>>> Implicit is way faster to compute, the system itself also settles far
>>> quicker, but it's considered more inaccurate and harder to optimize for
>>> GPU. It's also possible to have a hybrid approach, when the whole system
>>> is solvated implicitly, but select solvent molecules are explicitly
>>> included in the model.
>>>
>>> In GROMACS implicit solvent is depreciated, so you should either use
>>> explicit solvent, or pick a different MD engine if you want implicit.
>>> 23.12.2016 18:00, gromacs.org_gmx-users-request at maillist.sys.kth.se
>>> ?????:
>>> Message: 1
>>> Date: Fri, 23 Dec 2016 16:25:33 +0530
>>> From: Syed Azeem<syedazeemullah186 at gmail.com>
>>> To: "gromacs.org_gmx-users"
>>>       <gromacs.org_gmx-users at maillist.sys.kth.se>
>>> Subject: [gmx-users] Implicit and Explicit solvation
>>> Message-ID:
>>>
>>> <CAJnO2SBr39H+pgx0cb-FCfbvRGiSRCGqE0ddXdj4_F1ph2ehiA at mail.gmail.com>
>>> Content-Type: text/plain; charset=UTF-8
>>>
>>> Hi all,
>>>
>>> What's the difference between Implicit and Explicit solvation?
>>> Is there any difference in setting up the system for simulation?
>>> Which is computationally effiecient?
>>>
>>> Thanks in advance
>>>
>>> Azeem
>
> --
> ==================================================