[gmx-users] Merging different topology files

[Justin Lemkul]

On 9/8/17 10:19 AM, Momin Ahmad wrote:
> Hi Justin,
>
> could you provide me a link to some tutorials that focus more on the 
> program structure than on the results of simulations? I did some 
> protein simulation tutorials that did not really help me in 
> understanding the software itself. Big thanks in advance.
>

I'll recommend my own:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

I have a couple examples of analysis, but I purposefully do not 
emphasize analysis/outcomes in my tutorials.  This one has lots of 
detail about what every program is doing, what the options mean, and 
what the structure of the topology is.  Beyond that, for learning about 
topologies, Chapter 5 of the manual is your best resource, as is Google 
(every problem you might encounter has been solved at least once before, 
I'm fairly sure).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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