Σχετ: [gmx-users] umbrella sampling

[Giovani Mancini]

Dear Justin,


Thank you very much for your immediate response to my e-mail.

I am trying to conduct umbrella sampling simulations of a molecule into a lipid bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is well-written and provide useful information of how to set up the system in GROMACS. 


Best regards


Grigoris



----- Αρχικό μήνυμα -----
Απο: Justin Lemkul <jalemkul at vt.edu>
Προς: Giovani Mancini <giovani_manc at yahoo.gr>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Κοιν.: 
Στάλθηκε: 5:29 μ.μ. Δευτέρα, 16 Ιουλίου 2012
Θεμα: Re: [gmx-users] umbrella sampling



On 7/16/12 10:25 AM, Giovani Mancini wrote:
> Dear Gromacs users,
> 
> I just read the tutorial by Justin Lemkul about umbrella sampling simulations along z-axis. My question is whether we need cylindrical confinement of the molecule that is pulling away from a reference molecule.
> Thanks in advance
> 

The tutorial is a very simple system designed to get users familiar with a basic workflow.  There are more elegant ways of doing umbrella sampling for more complicated systems.  Cylindrical restraints can be useful in some cases and are discussed in the manual.  Without knowing more about the system you're considering, it's hard to provide specific advice.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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