[gmx-users] Implicit and Explicit solvation
syedazeemullah186 at gmail.com
Tue Dec 27 13:15:40 CET 2016
Thank you so much for the info.
I'll perform the simulation with explicit solvent and calculate the free energy.
> 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
> energy to give the free energy of the system. The (unofficial) g_mmpbsa
> does this. It does not require additional simulations.
>>> 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>
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>>> 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
>>> <CAJnO2SBr39H+pgx0cb-FCfbvRGiSRCGqE0ddXdj4_F1ph2ehiA at mail.gmail.com>
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>>> 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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