normal How to decide bond length for coarse grained model

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2 years 5 months ago #5920 by subhamoy
In the martini 2007 paper its mentioned that the equilibrium bond length to be 0.47nm for all CG beads, with the exception of "S" beads which has equilibrium bond length of 0.43nm. But looking again at Table 2 where the topology of Cholesterol is mentioned the bond lengths between the CG particles are very different. Ex: between (1) SP1 and (2) SC1 is given to be 0.242nm. I was wondering how the value 0.242 was achieved?

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2 years 5 months ago #5957 by peterkroon
Hi,

all bond lengths are usually chosen to reproduce the atomistic distributions. In case of molecules such as cholesterol it is often optimized further such that the CG molecule reproduces the macroscopic behaviour. Be sure to read the paper by M N Melo (DOI 10.1063/1.4937783) if you're going to use cholesterol in your simulations.
Also, the "bond lengths" you're quoting are the van der Waals diameters, which is a different thing altogether.

Peter

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2 years 3 months ago #6616 by subhamoy
Thanks for the clarification. My main doubt stemmed from the paper itself, in section 2.3 just below equation (3) it says " Rbond=σ=0.47nm" and " Kbond = 1250 kJ mol-1 nm-2 "

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