[gmx-users] FEP

[Michael Shirts]

FEP is a poorly defined term.  It can either mean 1) making small
changes 'alchemical' changes in the molecules and computing the free
energies by any method (BAR, TI, etc), or 2) it can mean specifically
computing the free energies by exponentially averaging the potential
energy differences.  Basically, using the exponential averaging
formula is a bad idea -- if you have code that only uses that method,
you can get decent results out if you are careful, but TI, BAR, and
MBAR are all better choices.

On Mon, Oct 10, 2011 at 10:58 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Steven Neumann wrote:
>>
>> Thank you guys! So, is there any tutorial in Gromacs for calculating free
>> energy of ligand binding using FEP?
>>
>
> TI or BAR are better methods for calculating binding free energies, I would
> think.  FEP is best for mutating between different species.
>
> -Justin
>
>> Steven
>>
>> On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    mohsen ramezanpour wrote:
>>
>>        Hi
>>        Please have a look at Dr.Justin tutorial page at the following
>> link:
>>
>>
>>  http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/index.html
>>
>>  <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html>
>>
>>
>>    This tutorial is not for FEP explicitly, but may be of some use.
>>     There is discussion on using the BAR algorithm for binding free
>>    energy calculations.
>>
>>    -Justin
>>
>>        Cheers
>>
>>
>>        On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann
>>        <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>>        <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>__>
>>        wrote:
>>
>>           Hi Gmx Users,
>>                Can you suggest some reading and some tutorial in
>>        calculations of
>>           binding free energy (ligand binding) in Gromacs? ?I want to
>>        use Free
>>           Energy Perturbation method.
>>                Steven
>>           --
>>           gmx-users mailing list    gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>
>>           <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>
>>           http://lists.gromacs.org/__mailman/listinfo/gmx-users
>>        <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>           Please search the archive at
>>           http://www.gromacs.org/__Support/Mailing_Lists/Search
>>        <http://www.gromacs.org/Support/Mailing_Lists/Search> before
>>        posting!
>>           Please don't post (un)subscribe requests to the list. Use the
>>           www interface or send it to gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>           <mailto:gmx-users-request at __gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>.
>>
>>           Can't post? Read
>>        http://www.gromacs.org/__Support/Mailing_Lists
>>        <http://www.gromacs.org/Support/Mailing_Lists>
>>
>>
>>
>>    --     ==============================__==========
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>>    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>>    ==============================__==========
>>
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/__mailman/listinfo/gmx-users
>>    <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>    Please search the archive at
>>    http://www.gromacs.org/__Support/Mailing_Lists/Search
>>    <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>>    interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>    Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>>    <http://www.gromacs.org/Support/Mailing_Lists>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>