[gmx-users] choice of forcefield

[Mark Abraham]

You'll still need to do some reading. If your moieties have never been used
in all-atom simulations, you'll have a big task of parameterization, or
have to accept some approximation in your model. Even if they have been
used, you'll want to read up on how they were parameterized and whether
they've been shown to work well. Search the literature!

Mark


On Tue, May 28, 2013 at 6:12 PM, Revthi Sanker <revthi.sanker at yahoo.com>wrote:

>
>
> Dear Sir,
> Thank
>  you so much for your reply. To be specific, my system has only four
> lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I
> was not able to get all atom parameters for these lipids from the lipid
> book( only united atom parameters were available). So I had resorted to
> using united atom for the whole system. But I am afraid if I am missing
> out on some crucial protein-drug interactions because of this united
> atom consideration.
> Kindly guide me in this regard.
> Thank you so much once again.
>
> Yours sincerely,
> Revathi
> M.S.Research Scholar
> Indian Institute of Technology Madras
> India
>
>
> --- On Tue, 28/5/13, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] choice of forcefield
> To: gmx-users at gromacs.org
> Date: Tuesday, 28 May, 2013, 1:30 PM
>
> On 2013-05-28 14:39, massimo sandal wrote:
> > What other people do?
>
> Read literature. Gromacs allows you to choose many. If you need detailed
> results use an atomistic force field.
> >
> >
> > 2013/5/28 Dr. Vitaly Chaban <vvchaban at gmail.com>
> >
> >> In my mind, MARTINI is a decent option to build your particular topology
> >> upon.
> >>
> >> Dr. Vitaly Chaban
> >>
> >>
> >> On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker <revthi.sanker at yahoo.com
> >>> wrote:
> >>
> >>> Dear all,
> >>> I am a beginner to performing simulations and my system consists of
> >>> protein+ cholesteryl ester +phospholipid and drug. Papers involving
> >> lipids
> >>> are in general united atom, while those involving drug-protein systems
> >> are
> >>> all-atom mostly. Kindly suggest me which of these, all-atom or united
> >> atom
> >>> should I be using for my system.
> >>>
> >>> Thanks for your help in advance
> >>> Yours sincerely,
> >>> Revathi
> >>> M.S. Research Scholar
> >>> Indian Institute of Technology,Madras
> >>> India
> >>> --
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> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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