[gmx-users] Umbrella Sampling - Justin tutorial

[Steven Neumann]

Thank you Justin! That helped a lot!

Steven

On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>> Thank you Justin, now I get what you mean!
>> As I understood I should pick just one frame untill 189 ps (when
>> dissociation occured) - does it matter which one I will choose on the final
>> binding free energy?
>>
>
> The free energy minimum should (theoretically) be when the peptides are
> still interacting, i.e. at time zero.  Use this frame and base the spacing
> off of it.
>
>
> Then spacing should be 0.2 nm. Right? But how is it possible to do spacing
>> like this from such results of summary_distances.dat:
>>
>> 189 0.5769072
>>
>> 190 0.5753590
>>
>> 191 0.5711223
>>
>> 192 0.5719844
>>
>> 193 0.5856807
>>
>> 194 0.5886649
>>
>> 195 0.5958101
>>
>> .......
>>
>> 211 0.7111782
>>
>> 212 0.7322708
>>
>> 213 0.7675126
>>
>> ...
>>
>> 378 4.2101626
>>
>> 379 4.1993918
>>
>> 380 4.2223649
>>
>> ......
>>
>> 500 5.48839
>>
>> Do you mean the approximate valueof 0.2 nm spacing? As it would be
>> difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until
>> e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until
>> 5nm?
>>
>>
> Choose approximate values.
>
> My protocol of uneven spacing was necessary to refine the energy minimum
> for the suitable data for the paper.  I kept the tutorial simple; you
> should still achieve a reasonable result.  Uneven spacing is uncommon in
> the literature, so I did not want to give anyone the impression that it was
> a standard protocol, leaving it as an exercise for the reader to understand
> the paper and the motivation for uneven spacing.
>
>
> -Justin
>
> --
> ==============================**==========
>
> 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<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/20111116/3b6629ba/attachment.html>