[gmx-users] Implicit and Explicit solvation
jalemkul at vt.edu
Mon Dec 26 21:50:28 CET 2016
On 12/23/16 10:22 PM, Syed Azeem wrote:
> 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?
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.
> 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
>> 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>
>> 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
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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