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

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 9 14:22:21 CEST 2009

ms wrote:
> Hi,
> 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.

So, to clarify, this is an already-existing CG model that you simply want to use 
for simulations in Gromacs?  It is then rather easy.  You need to define all 
appropriate force field files (nb.itp, bon.itp, .atp, etc), and perhaps .rtp 
files if you can also come up with a way to define an appropriate CG input for 


> Thanks a lot!
> Massimo
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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