[gmx-users] Implicit and Explicit solvation
syedazeemullah186 at gmail.com
Sat Dec 24 04:22:15 CET 2016
Thanks Tyugashev for your response.
It was a reviewer suggestion to run our protein-peptide docked complex
in a continuum solvent and compute their free energies of association.
After this, I came across MMPBSA
and its GROMACS tool g_mmpbsa.
Is this not based on Implicit solvation? How can I perform it to
validate my docking?
Thanks in advance
>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
>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
> <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
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