[gmx-users] Re: doubt about your Umbrella Sampling tutorial

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> Dear Justin,
> my name is Rebeca and I am a postdoctoral student in Santiago de 
> Compostela University. Sorry for disturbing you to your personal mail, I 
> have tried to post to the Gromacs-list first, but I did not get any answer.

I was traveling and not paying much attention to messages across the list.  I 
will CC this reply to the list in the hopes that it is useful to others, as well.

> I am trying to obtain the PMF from Umbrella Sampling of the process of 
> separating two monomers of a dimer, following your tutorial, and I have 
> a pair of doubts:
> 
> 1)In this tutorial the generation of configurations is done using a .mdp 
> file for pulling one chain from another, but is it possible to generate 
> the configurations for Umbrella Sampling "by hand", I mean, changing the 
> z coordinate of the monomer I want to move, then solvating and then 
> minimizing these configurations? Is there any problem with this protocol 
> for the obtaining of the configurations?
> 

No problem at all.  The tutorial is but one possible method.

> 2) I have noticed that you use restraints in the md_umbrella.mdp for the 
> fixed chain. Is that correct? I can understand the restraints in the 
> pulling simulations for generate starting configurations, but once you 
> have the configurations, is is necessary to restrain one part of the 
> system?
> 

Not usually.  The tutorial presents a special case.

> Thanks a lot in advance for your help with this topic, and thank you 
> very much also for publishing this interesting tutorial. There was 
> nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I 
> think it is more than wellcome for all Gromacs users!

Glad they're useful :)

-Justin

> Best wishes,
> Rebeca.
> 
> Dr. Rebeca García Fandiño
> Department of Organic Chemistry and Center for Research in Biological 
> Chemistry
> and Molecular Materials
> Santiago de Compostela University
> E-15782 Santiago de Compostela (Spain)
> e-mail: rebeca.garcia.fandino at usc.es
> Phone: 34-981563100 ext 15760
> 
> 
> 
> 
> 
> 
> 

-- 
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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

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