[gmx-users] Umbrella Sampling - spacing

Steven Neumann s.neumann08 at gmail.com
Wed Feb 22 18:01:38 CET 2012

Thank you!

On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Steven Neumann wrote:
>> Dear Gmx Users, Dear Justin,
>>  I run pulling of my ligand away from my protein. Then I used Justin perl
>> script to extract distances for umbrella sampling windows between my ligand
>> and crucial residue of my protein (Isoleucine). The number of hydrogen
>> bonds between ligand and protein during the pulling is app. 3 at the
>> begining, then 4 in some frames and then obviously zero (when ligand
>> dissociated).
>> Would you use the 1st frame as a starting window when number of hbonds is
>> 3 or further window when this is number is 4?
> Assuming the first frame represents a fully-bound configuration, you
> should start there.  I'm guessing you're trying to determine the DeltaG of
> binding for your ligand.  If you define an arbitrary reaction coordinate,
> you get an arbitrary answer.  Starting and ending points dictate the value
> of DeltaG (since it is a state function).
> Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where
>> interactions are via hydrogen bonds and hydrophobic interactions only?
> Most systems interact via hydrogen bonds and hydrophobic interactions.
> Generally, 0.2 nm is a decent starting point, but should by no means be
> viewed as any sort of universal standard.  It worked for me in my tutorial,
> it may not work for others.  Consult the literature for similar systems and
> proceed.  If you find under-sampled regions along the reaction coordinate,
> it is trivial to add a new window.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> 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
> 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.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120222/73d6b890/attachment.html>

More information about the gromacs.org_gmx-users mailing list