[gmx-users] Tips and tricks to make your own coarse-grained model?

ms devicerandom at gmail.com
Fri Oct 9 14:11:26 CEST 2009


First of all, I am new to Gromacs and quite new to the MD field (I had a
read of the Daan-Frenkel book and played very little with custom CG
models - I used to be an experimental guy), so please bear with me if
questions happen to be naive.

My aim is to re-implement a formerly standalone CG model by mean of gmx.
It seems that gmx is well suited to the task; however I understand that
there is an incredible number of pitfalls where a newbie fall in.

I am currently reading and re-reading the manual, looking at the online
docs and tutorials. But most of information, understandably, refer to
all-atom modeling and there is little on how to build your own model on gmx.

Maybe my googling skills are not as good as once they were -in this case
can anyone point me to any page where this kind of task is documented?

If such a page there isn't (and even if there is), I would appreciate a
lot if anyone of you can share your wisdom on best practices, pitfalls,
things to know etc. before diving head-on in such an endeavour.

Thanks a lot!


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