[gmx-users] MD Simulation of DPPC Lipid Bilayer

[Justin A. Lemkul]

Quoting Nancy <nancy5villa at gmail.com>:

> Hello,
>
> I am new to Gromacs, but have prior experience with MD simulations.  I'd
> like to setup and run a simulation of hydrated
> dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature
> (~298 K).  Are there tutorials that provide step-by-step instructions on how
> to do this?
>

Not directly, but there are several resources available.  Step 1 should
certainly be Chapter 5 of the manual, to understand how to construct the
topology of your system, since pdb2gmx will not do it for you.  Other than
that, there are general references online:

http://oldwiki.gromacs.org/index.php/Membrane_Simulations

There is also a plethora of question/answer threads in the list archive, which
can be searched through the online interface:

http://oldwww.gromacs.org/swish-e/search/search2.php

Structures and topologies can be downloaded from a number of research group
webpages, many of which are cited in the literature and mentioned in the
archived discussions.

-Justin

> Thank you.
>
> Nancy
>



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Justin A. Lemkul
Graduate Research Assistant
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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