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.fand...@usc.es
Phone: 34-981563100 ext 15760
--
========================================
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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